From missy at be.to Tue Feb 1 22:51:56 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Wed, 02 Feb 2011 12:51:56 +0900 Subject: [BioRuby] Rakefiles for the Dindel workflow Message-ID: <4D48D4DC.3020808@be.to> Hi all, I wrote a rakefile for the Dindel workflow. Dindel is a toolkit to call small indels from mapped short-read data (BAM files). See http://www.sanger.ac.uk/resources/software/dindel/ . The rakefile is available at https://github.com/misshie/RakefileDindel . I think my rakefile is a good example of "dynamic task definition". During Stage 3 of the workflow, Dindel generates over 300 files for exome data. Although the file naming rule is known before running rake, the number of files to be generated is unknown at the time. van der Aalst et al. (2003) have shown this pattern as "pattern 14: multiple instances with a priori runtime knowledge". Rakefiles can describe this pattern using Rake::Task#invoke. Furthermore, this rakefile demonstrates effectiveness of Pwrake. Stage 3 is a typical embarrassingly parallel problem. To improve rakefile readability, I separated a Rakefile into Rakefile, Rakefile.invoke, and Rakefile.helper. Rakefile is workflow description. Rakefile.invoke is command-lines to invoke tools. Rakefile.helper has helper methods making Rakefile simpler. Previously Yannick Wurm has shown a rakefile "cdsToAlignmentToTree" at https://github.com/yannickwurm/tidbits/ . The rakefile handles exceptions carefully. Mine does not. Yannick's approach is important because sometimes error messages in rakefiles are not intuitive. So far, my workflow does not use BioRuby at all. Raoul Bonnal have suggested BioRuby-rake integration replying Yannick's post. Introducing modular task definition to rake is what we need but not very easy because each workflow step in a rakefiles is linked too tight. Introducing a BioRuby plug-in to support common helper methods simplifying rakefiles seems easier. It may contain my Rakefile.helper, and Yannick's helper methods and exception handling. I will try to write a small plug-in for a while. Sincerely yours, Hiro. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From bonnalraoul at ingm.it Wed Feb 2 04:41:47 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 2 Feb 2011 10:41:47 +0100 Subject: [BioRuby] Rakefiles for the Dindel workflow In-Reply-To: <4D48D4DC.3020808@be.to> References: <4D48D4DC.3020808@be.to> Message-ID: <5881720A-141D-41A5-A872-0FB004DA9C5D@ingm.it> Hi Hiro, seems an interesting approach, we could discuss this e-mail tomorrow during the irc meeting. is it fine for you ? I can't catch how do you use pwrake, sorry probably I missed something, I mean the benefit. On 02/feb/2011, at 04.51, MISHIMA, Hiroyuki wrote: > Hi all, > > I wrote a rakefile for the Dindel workflow. Dindel is a toolkit to call > small indels from mapped short-read data (BAM files). See > http://www.sanger.ac.uk/resources/software/dindel/ . > > The rakefile is available at https://github.com/misshie/RakefileDindel . > > I think my rakefile is a good example of "dynamic task definition". > During Stage 3 of the workflow, Dindel generates over 300 files for > exome data. Although the file naming rule is known before running rake, > the number of files to be generated is unknown at the time. > > van der Aalst et al. (2003) have shown this pattern as "pattern 14: > multiple instances with a priori runtime knowledge". Rakefiles can > describe this pattern using Rake::Task#invoke. > > Furthermore, this rakefile demonstrates effectiveness of Pwrake. Stage 3 > is a typical embarrassingly parallel problem. > > To improve rakefile readability, I separated a Rakefile into Rakefile, > Rakefile.invoke, and Rakefile.helper. Rakefile is workflow description. > Rakefile.invoke is command-lines to invoke tools. Rakefile.helper has > helper methods making Rakefile simpler. > > Previously Yannick Wurm has shown a rakefile "cdsToAlignmentToTree" at > https://github.com/yannickwurm/tidbits/ . The rakefile handles > exceptions carefully. Mine does not. Yannick's approach is important > because sometimes error messages in rakefiles are not intuitive. > > So far, my workflow does not use BioRuby at all. Raoul Bonnal have > suggested BioRuby-rake integration replying Yannick's post. Introducing > modular task definition to rake is what we need but not very easy > because each workflow step in a rakefiles is linked too tight. > > Introducing a BioRuby plug-in to support common helper methods > simplifying rakefiles seems easier. It may contain my Rakefile.helper, > and Yannick's helper methods and exception handling. > > I will try to write a small plug-in for a while. > > Sincerely yours, > Hiro. > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- R.J.P.B. From bonnalraoul at ingm.it Wed Feb 2 04:42:37 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 2 Feb 2011 10:42:37 +0100 Subject: [BioRuby] SRA and NCBI Message-ID: <02654276-648A-47CF-B24E-B05E50FB8428@ingm.it> Take a look for downloading data from ncbi http://www.ncbi.nlm.nih.gov/books/NBK47540/ Do we want to support sra or just the tool kit ? -- R.J.P.B. From missy at be.to Wed Feb 2 08:48:36 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Wed, 02 Feb 2011 22:48:36 +0900 Subject: [BioRuby] Rakefiles for the Dindel workflow In-Reply-To: <5881720A-141D-41A5-A872-0FB004DA9C5D@ingm.it> References: <4D48D4DC.3020808@be.to> <5881720A-141D-41A5-A872-0FB004DA9C5D@ingm.it> Message-ID: <4D4960B4.3090003@be.to> Hi, I will attend tomorrow's irc meeting. See you all at #bioruby. And, the benefit to use Pwrake is the followings: Rakefiles for Rake and Pwrake is fully compatible. However, Pwrake automatically finds "embarrassingly parallel" steps and smartly distributes processes via ssh. For example, when nodefile is "localhost 16", Pwrake tries to keep running 16 processes simultaneously. The function is indispensable to run more than 300 processes in Dindel's stage 3. Sincerely yours, Hiro Raoul Bonnal wrote (2011/02/02 18:41): > Hi Hiro, seems an interesting approach, we could discuss this e-mail > tomorrow during the irc meeting. is it fine for you ? > > I can't catch how do you use pwrake, sorry probably I missed > something, I mean the benefit. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From mictadlo at gmail.com Thu Feb 3 03:16:25 2011 From: mictadlo at gmail.com (Michal) Date: Thu, 03 Feb 2011 18:16:25 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: References: <4D454E91.1080604@gmail.com> Message-ID: <4D4A6459.5050205@gmail.com> Dear Raoul, I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: $ tar xvfz ruby-1.9.2-p136.tar.gz $ cd ruby-1.9.2-p136/ $ ./configure --prefix=/home/mictadlo/apps/ruby $ make $ make install $ vim ~/.bashrc export APPS=/home/mictadlo/apps export RUBY_HOME=$APPS/ruby export LD_LIBRARY_PATH=/RUBY_HOME/lib PATH=$RUBY_HOME/bin:$PATH $ . ~/.bashrc $ ruby -v ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] $ gem install ffi Building native extensions. This could take a while... Successfully installed ffi-1.0.5 1 gem installed Installing ri documentation for ffi-1.0.5... Installing RDoc documentation for ffi-1.0.5... ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ remote: Counting objects: 92, done. remote: Compressing objects: 100% (84/84), done. remote: Total 92 (delta 21), reused 0 (delta 0) Unpacking objects: 100% (92/92), done. ~/Downloads/git/bioruby-samtools$ rake test (in /home/mictadlo/Downloads/git/bioruby-samtools) rake aborted! no such file to load -- bundler :29:in `require' :29:in `require' /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' /home/mictadlo/apps/ruby/bin/rake:31:in `
' What did I wrong? Thank you in advance. Michal On 01/31/2011 08:11 PM, Raoul Bonnal wrote: > Dear Michal, > please check this out: > > https://github.com/helios/bioruby-samtools > > This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. > I need to test the linux library because I'm developing under osx. > If the libbam.a is wrong please give me the right one and I'll add it to the repo. > Also note that the library has been compiled for 64bit. > > Ciao! > > On 30/gen/2011, at 12.42, Michal wrote: > >> Hi, >> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >> >> What did I wrong? >> >> Michal >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > -- > R.J.P.B. > > > > > From mictadlo at gmail.com Thu Feb 3 04:55:07 2011 From: mictadlo at gmail.com (Michal) Date: Thu, 03 Feb 2011 19:55:07 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> Message-ID: <4D4A7B7B.2000103@gmail.com> Hi Philipp, Bundler fix one problem, but I have got a new one: $ gem install bundler Successfully installed bundler-1.0.10 1 gem installed Installing ri documentation for bundler-1.0.10... Installing RDoc documentation for bundler-1.0.10... ~/Downloads/git/bioruby-samtools$ rake test (in /home/uqmlore1/Downloads/git/bioruby-samtools) Could not find bio-1.4.1 in any of the sources Run `bundle install` to install missing gems $ irb irb(main):001:0> require "bio" => true irb(main):002:0> exit $ bioruby Loading config (/home/uqmlore1/.bioruby/shell/session/config) ... done Loading object (/home/uqmlore1/.bioruby/shell/session/object) ... Error: Failed to load (/home/uqmlore1/.bioruby/shell/session/object) : marshal data too short done . . . B i o R u b y i n t h e s h e l l . . . Version : BioRuby 1.4.1 / Ruby 1.9.2 Thank you in advance. Michal On 02/03/2011 07:03 PM, Philipp Comans wrote: > Try gem install bundler > > Am 03.02.2011 um 09:16 schrieb Michal: > >> Dear Raoul, >> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: >> $ tar xvfz ruby-1.9.2-p136.tar.gz >> $ cd ruby-1.9.2-p136/ >> $ ./configure --prefix=/home/mictadlo/apps/ruby >> $ make >> $ make install >> $ vim ~/.bashrc >> export APPS=/home/mictadlo/apps >> export RUBY_HOME=$APPS/ruby >> export LD_LIBRARY_PATH=/RUBY_HOME/lib >> PATH=$RUBY_HOME/bin:$PATH >> $ . ~/.bashrc >> $ ruby -v >> ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] >> >> $ gem install ffi >> Building native extensions. This could take a while... >> Successfully installed ffi-1.0.5 >> 1 gem installed >> Installing ri documentation for ffi-1.0.5... >> Installing RDoc documentation for ffi-1.0.5... >> >> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git >> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ >> remote: Counting objects: 92, done. >> remote: Compressing objects: 100% (84/84), done. >> remote: Total 92 (delta 21), reused 0 (delta 0) >> Unpacking objects: 100% (92/92), done. >> >> ~/Downloads/git/bioruby-samtools$ rake test >> (in /home/mictadlo/Downloads/git/bioruby-samtools) >> rake aborted! >> no such file to load -- bundler >> :29:in `require' >> :29:in `require' >> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' >> /home/mictadlo/apps/ruby/bin/rake:31:in `
' >> >> What did I wrong? >> >> Thank you in advance. >> >> Michal >> >> On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >>> Dear Michal, >>> please check this out: >>> >>> https://github.com/helios/bioruby-samtools >>> >>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. >>> I need to test the linux library because I'm developing under osx. >>> If the libbam.a is wrong please give me the right one and I'll add it to the repo. >>> Also note that the library has been compiled for 64bit. >>> >>> Ciao! >>> >>> On 30/gen/2011, at 12.42, Michal wrote: >>> >>>> Hi, >>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >>>> >>>> What did I wrong? >>>> >>>> Michal >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> -- >>> R.J.P.B. >>> >>> >>> >>> >>> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby From tomoakin at kenroku.kanazawa-u.ac.jp Thu Feb 3 05:10:28 2011 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Thu, 3 Feb 2011 19:10:28 +0900 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4A6459.5050205@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> Message-ID: <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> Hi, As it says. > Run `bundle install` to install missing gems $ bundle install will install all other required gems. The next thing to do is for the error: /home/tomoaki/ruby192p136/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/ library.rb:75:in `block in ffi_lib': Could not open library '/home/ tomoaki/bioruby-samtools/lib/bio/db/sam/external/libbam.a': Its natural that a dynamic library should be made for the purpose as is in Mac OS X. $ make dylib in the latest samtools and copy libbam.so.1 to bioruby-samtools/lib/ bio/db/sam/external/ ------------CUT diff --git a/lib/bio/db/sam/external/libbam.a b/lib/bio/db/sam/ external/libbam.a index 0f231ef..aa1b225 100644 Binary files a/lib/bio/db/sam/external/libbam.a and b/lib/bio/db/sam/ external/libbam.a differ diff --git a/lib/bio/db/sam/library.rb b/lib/bio/db/sam/library.rb index bb78515..e9f8b6e 100644 --- a/lib/bio/db/sam/library.rb +++ b/lib/bio/db/sam/library.rb @@ -9,7 +9,7 @@ module Bio #TODO refactor this piece of code in all the files lib_os = case RUBY_PLATFORM when /linux/ - 'a' + 'so.1' when /darwin/ 'dylib' when /windows/ @@ -22,4 +22,4 @@ module Bio end #Library end #Sam end #DB -end #Bio \ No newline at end of file +end #Bio ------------CUT Then finally reached this state $ ~/ruby192p136/bin/rake (in /home/tomoaki/bioruby-samtools) /home/tomoaki/ruby192p136/bin/ruby -I"lib:lib:test" "/home/tomoaki/ ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio- samtools.rb" Loaded suite /home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/ rake_test_loader Started F Finished in 0.000321 seconds. 1) Failure: test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: hey buddy, you should probably rename this file and start testing for real Loading seems ok. I'm not sure if this is bad or ok. Best regards -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan On 2011/02/03, at 17:16, Michal wrote: > Dear Raoul, > I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 > 64bit in the following way: > $ tar xvfz ruby-1.9.2-p136.tar.gz > $ cd ruby-1.9.2-p136/ > $ ./configure --prefix=/home/mictadlo/apps/ruby > $ make > $ make install > $ vim ~/.bashrc > export APPS=/home/mictadlo/apps > export RUBY_HOME=$APPS/ruby > export LD_LIBRARY_PATH=/RUBY_HOME/lib > PATH=$RUBY_HOME/bin:$PATH > $ . ~/.bashrc > $ ruby -v > ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] > > $ gem install ffi > Building native extensions. This could take a while... > Successfully installed ffi-1.0.5 > 1 gem installed > Installing ri documentation for ffi-1.0.5... > Installing RDoc documentation for ffi-1.0.5... > > ~/Downloads/git$ git clone https://github.com/helios/bioruby- > samtools.git > Initialized empty Git repository in /home/mictadlo/Downloads/git/ > bioruby-samtools/.git/ > remote: Counting objects: 92, done. > remote: Compressing objects: 100% (84/84), done. > remote: Total 92 (delta 21), reused 0 (delta 0) > Unpacking objects: 100% (92/92), done. > > ~/Downloads/git/bioruby-samtools$ rake test > (in /home/mictadlo/Downloads/git/bioruby-samtools) > rake aborted! > no such file to load -- bundler > :29:in `require' > :29:in `require' > /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in ` (required)>' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in > `raw_load_rakefile' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in > load_rakefile' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in > `standard_exception_handling' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in > `load_rakefile' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' > /home/mictadlo/apps/ruby/bin/rake:31:in `
' > > What did I wrong? > > Thank you in advance. > > Michal > > On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >> Dear Michal, >> please check this out: >> >> https://github.com/helios/bioruby-samtools >> >> This is the inital port of samtools-ruby as plugin. It comes with >> library for osx and linux, no windows. >> I need to test the linux library because I'm developing under osx. >> If the libbam.a is wrong please give me the right one and I'll add >> it to the repo. >> Also note that the library has been compiled for 64bit. >> >> Ciao! >> >> On 30/gen/2011, at 12.42, Michal wrote: >> >>> Hi, >>> I have tried to install samtools-ruby on ruby 1.9.2, but I have >>> failed. I have already posted this problem on https://github.com/ >>> homonecloco/samtools-ruby/issues#issue/3 , but I have not got any >>> response. >>> >>> What did I wrong? >>> >>> Michal >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> -- >> R.J.P.B. >> >> >> >> >> > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From mictadlo at gmail.com Thu Feb 3 06:23:40 2011 From: mictadlo at gmail.com (Michal) Date: Thu, 03 Feb 2011 21:23:40 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: <1BC9C29B-EE9E-4F9A-B96B-27FD341204E1@googlemail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <4D4A7B7B.2000103@gmail.com> <1BC9C29B-EE9E-4F9A-B96B-27FD341204E1@googlemail.com> Message-ID: <4D4A903C.2030807@gmail.com> Hi Philipp, Bundle solved this problem, but after rake install I can not call rake test. $ bundle install Fetching source index for http://rubygems.org/ Using rake (0.8.7) Installing bio (1.4.1) Using bundler (1.0.10) Using ffi (1.0.5) Installing git (1.2.5) Installing jeweler (1.5.2) Installing rcov (0.9.9) with native extensions Installing shoulda (2.11.3) Your bundle is complete! Use `bundle show [gemname]` to see where a bundled gem is installed. $ rake install (in /home/mictadlo/Downloads/git/bioruby-samtools) WARNING: no rubyforge_project specified Successfully built RubyGem Name: bio-samtools Version: 0.0.0 File: bio-samtools-0.0.0.gem Executing "ruby -S gem install ./pkg/bio-samtools-0.0.0.gem": ruby -S gem install ./pkg/bio-samtools-0.0.0.gem Successfully installed bio-samtools-0.0.0 1 gem installed Installing ri documentation for bio-samtools-0.0.0... Installing RDoc documentation for bio-samtools-0.0.0... $ rake test (in /home/mictadlo/Downloads/git/bioruby-samtools) /home/mictadlo/apps/ruby/bin/ruby -I"lib:lib:test" "/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in `block in ffi_lib': Could not open library '/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.a': /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.a: invalid ELF header (LoadError) from /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in `map' from /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in `ffi_lib' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:12:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:8:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:7:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:6:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:5:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `' from test/test_bio-samtools.rb:1:in `require' from test/test_bio-samtools.rb:1:in `' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `load' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `block in
' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `each' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `
' rake aborted! Command failed with status (1): [/home/mictadlo/apps/ruby/bin/ruby -I"lib:l...] /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:993:in `block in sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1027:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:115:in `block (2 levels) in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1110:in `verbose' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:100:in `block in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `block in execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:595:in `block in invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/monitor.rb:201:in `mon_synchronize' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:588:in `invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:581:in `invoke' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2041:in `invoke_task' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block (2 levels) in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2013:in `top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1992:in `run' /home/mictadlo/apps/ruby/bin/rake:31:in `
' What did I wrong? Michal On 02/03/2011 08:06 PM, Philipp Comans wrote: > Hi Michal, > have you tried running > > bundle install > rake install > > In order to install the missing gems? > I see that you have bio installed but maybe it's missing something else. > > The error about "marshal data too short" went through the mailing list a few days ago, I think it is currently being worked on. > > Hope that helps! > > Best, > > Philipp > > Am 03.02.2011 um 10:55 schrieb Michal: > >> Hi Philipp, >> Bundler fix one problem, but I have got a new one: >> >> $ gem install bundler >> Successfully installed bundler-1.0.10 >> 1 gem installed >> Installing ri documentation for bundler-1.0.10... >> Installing RDoc documentation for bundler-1.0.10... >> >> ~/Downloads/git/bioruby-samtools$ rake test >> (in /home/uqmlore1/Downloads/git/bioruby-samtools) >> Could not find bio-1.4.1 in any of the sources >> Run `bundle install` to install missing gems >> >> $ irb >> irb(main):001:0> require "bio" >> => true >> irb(main):002:0> exit >> >> $ bioruby >> Loading config (/home/uqmlore1/.bioruby/shell/session/config) ... done >> Loading object (/home/uqmlore1/.bioruby/shell/session/object) ... Error: Failed to load (/home/uqmlore1/.bioruby/shell/session/object) : marshal data too short >> done >> >> . . . B i o R u b y i n t h e s h e l l . . . >> >> Version : BioRuby 1.4.1 / Ruby 1.9.2 >> >> >> Thank you in advance. >> >> Michal >> >> >> On 02/03/2011 07:03 PM, Philipp Comans wrote: >>> Try gem install bundler >>> >>> Am 03.02.2011 um 09:16 schrieb Michal: >>> >>>> Dear Raoul, >>>> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: >>>> $ tar xvfz ruby-1.9.2-p136.tar.gz >>>> $ cd ruby-1.9.2-p136/ >>>> $ ./configure --prefix=/home/mictadlo/apps/ruby >>>> $ make >>>> $ make install >>>> $ vim ~/.bashrc >>>> export APPS=/home/mictadlo/apps >>>> export RUBY_HOME=$APPS/ruby >>>> export LD_LIBRARY_PATH=/RUBY_HOME/lib >>>> PATH=$RUBY_HOME/bin:$PATH >>>> $ . ~/.bashrc >>>> $ ruby -v >>>> ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] >>>> >>>> $ gem install ffi >>>> Building native extensions. This could take a while... >>>> Successfully installed ffi-1.0.5 >>>> 1 gem installed >>>> Installing ri documentation for ffi-1.0.5... >>>> Installing RDoc documentation for ffi-1.0.5... >>>> >>>> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git >>>> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ >>>> remote: Counting objects: 92, done. >>>> remote: Compressing objects: 100% (84/84), done. >>>> remote: Total 92 (delta 21), reused 0 (delta 0) >>>> Unpacking objects: 100% (92/92), done. >>>> >>>> ~/Downloads/git/bioruby-samtools$ rake test >>>> (in /home/mictadlo/Downloads/git/bioruby-samtools) >>>> rake aborted! >>>> no such file to load -- bundler >>>> :29:in `require' >>>> :29:in `require' >>>> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' >>>> /home/mictadlo/apps/ruby/bin/rake:31:in `
' >>>> >>>> What did I wrong? >>>> >>>> Thank you in advance. >>>> >>>> Michal >>>> >>>> On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >>>>> Dear Michal, >>>>> please check this out: >>>>> >>>>> https://github.com/helios/bioruby-samtools >>>>> >>>>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. >>>>> I need to test the linux library because I'm developing under osx. >>>>> If the libbam.a is wrong please give me the right one and I'll add it to the repo. >>>>> Also note that the library has been compiled for 64bit. >>>>> >>>>> Ciao! >>>>> >>>>> On 30/gen/2011, at 12.42, Michal wrote: >>>>> >>>>>> Hi, >>>>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >>>>>> >>>>>> What did I wrong? >>>>>> >>>>>> Michal >>>>>> _______________________________________________ >>>>>> BioRuby Project - http://www.bioruby.org/ >>>>>> BioRuby mailing list >>>>>> BioRuby at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>>> -- >>>>> R.J.P.B. >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnalraoul at ingm.it Thu Feb 3 06:56:00 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Thu, 3 Feb 2011 12:56:00 +0100 Subject: [BioRuby] samtools-ruby In-Reply-To: <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> Message-ID: <970B13D0-ADD4-478E-ABDB-6DBB7CD16DC7@ingm.it> Thanks Tomoaki I missed the linux lib sorry, could you send me that library I'll add it to the repo. so.1 fixed On 03/feb/2011, at 11.10, Tomoaki NISHIYAMA wrote: > Hi, > > As it says. > >> Run `bundle install` to install missing gems > > > $ bundle install > > will install all other required gems. > > The next thing to do is for the error: > > /home/tomoaki/ruby192p136/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in `block in ffi_lib': Could not open library '/home/tomoaki/bioruby-samtools/lib/bio/db/sam/external/libbam.a': > > Its natural that a dynamic library should be made for the purpose as is in Mac OS X. > > $ make dylib > in the latest samtools and copy libbam.so.1 to bioruby-samtools/lib/bio/db/sam/external/ > > > ------------CUT > diff --git a/lib/bio/db/sam/external/libbam.a b/lib/bio/db/sam/external/libbam.a > index 0f231ef..aa1b225 100644 > Binary files a/lib/bio/db/sam/external/libbam.a and b/lib/bio/db/sam/external/libbam.a differ > diff --git a/lib/bio/db/sam/library.rb b/lib/bio/db/sam/library.rb > index bb78515..e9f8b6e 100644 > --- a/lib/bio/db/sam/library.rb > +++ b/lib/bio/db/sam/library.rb > @@ -9,7 +9,7 @@ module Bio > #TODO refactor this piece of code in all the files > lib_os = case RUBY_PLATFORM > when /linux/ > - 'a' > + 'so.1' > when /darwin/ > 'dylib' > when /windows/ > @@ -22,4 +22,4 @@ module Bio > end #Library > end #Sam > end #DB > -end #Bio > \ No newline at end of file > +end #Bio > ------------CUT > > Then finally reached this state > > $ ~/ruby192p136/bin/rake > (in /home/tomoaki/bioruby-samtools) > /home/tomoaki/ruby192p136/bin/ruby -I"lib:lib:test" "/home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" > Loaded suite /home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader > Started > F > Finished in 0.000321 seconds. > > 1) Failure: > test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: > hey buddy, you should probably rename this file and start testing for real > > Loading seems ok. > I'm not sure if this is bad or ok. > > Best regards > -- > Tomoaki NISHIYAMA > > Advanced Science Research Center, > Kanazawa University, > 13-1 Takara-machi, > Kanazawa, 920-0934, Japan > > > On 2011/02/03, at 17:16, Michal wrote: > >> Dear Raoul, >> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: >> $ tar xvfz ruby-1.9.2-p136.tar.gz >> $ cd ruby-1.9.2-p136/ >> $ ./configure --prefix=/home/mictadlo/apps/ruby >> $ make >> $ make install >> $ vim ~/.bashrc >> export APPS=/home/mictadlo/apps >> export RUBY_HOME=$APPS/ruby >> export LD_LIBRARY_PATH=/RUBY_HOME/lib >> PATH=$RUBY_HOME/bin:$PATH >> $ . ~/.bashrc >> $ ruby -v >> ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] >> >> $ gem install ffi >> Building native extensions. This could take a while... >> Successfully installed ffi-1.0.5 >> 1 gem installed >> Installing ri documentation for ffi-1.0.5... >> Installing RDoc documentation for ffi-1.0.5... >> >> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git >> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ >> remote: Counting objects: 92, done. >> remote: Compressing objects: 100% (84/84), done. >> remote: Total 92 (delta 21), reused 0 (delta 0) >> Unpacking objects: 100% (92/92), done. >> >> ~/Downloads/git/bioruby-samtools$ rake test >> (in /home/mictadlo/Downloads/git/bioruby-samtools) >> rake aborted! >> no such file to load -- bundler >> :29:in `require' >> :29:in `require' >> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' >> /home/mictadlo/apps/ruby/bin/rake:31:in `
' >> >> What did I wrong? >> >> Thank you in advance. >> >> Michal >> >> On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >>> Dear Michal, >>> please check this out: >>> >>> https://github.com/helios/bioruby-samtools >>> >>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. >>> I need to test the linux library because I'm developing under osx. >>> If the libbam.a is wrong please give me the right one and I'll add it to the repo. >>> Also note that the library has been compiled for 64bit. >>> >>> Ciao! >>> >>> On 30/gen/2011, at 12.42, Michal wrote: >>> >>>> Hi, >>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >>>> >>>> What did I wrong? >>>> >>>> Michal >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> -- >>> R.J.P.B. >>> >>> >>> >>> >>> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > -- R.J.P.B. From missy at be.to Fri Feb 4 00:22:42 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Fri, 04 Feb 2011 14:22:42 +0900 Subject: [BioRuby] Rakefile for the GATK workflow Message-ID: <4D4B8D22.10502@be.to> Hi all, I did my assignment at last IRC meeting. 1) I updated the Workflows page in the BioRuby wiki. see http://bioruby.open-bio.org/wiki/Workflows I added Michael Barton's comment about Boson, and pointers to lists of job schedulers. 2) I uploaded another rakefile sample for the GATK workflow. see https://github.com/misshie/RakefileGATK Broad institutes's Genome Analysis Toolkit (GATK) is a toolkit to detect genomic variation (mainly SNVs) from mapped NGS short reads data (BAM files). It is consists of many Java programs and requires long command-line options. Moreover, GATK team changes their recommended workflow frequently because of active development. Thus well-organized workflow management is preferable. My rakefiles are still not well-organized. Not DRY. Please let me know your comment. Sincerely yours, Hiro. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From mictadlo at gmail.com Fri Feb 4 03:01:25 2011 From: mictadlo at gmail.com (Michal) Date: Fri, 04 Feb 2011 18:01:25 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> Message-ID: <4D4BB255.7030703@gmail.com> Hello, Still problems after the following steps: ~/Downloads/samtools-0.1.12a $ make dylib ~/Downloads/samtools-0.1.12a $ cp libbam.so.1 ../git/bioruby-samtools/lib/bio/db/sam/external/ ~/Downloads/samtools-0.1.12a $ ls ../git/bioruby-samtools/lib/bio/db/sam/external/ libbam.a libbam.dylib libbam.so.1 ~/Downloads/samtools-0.1.12a $ cat ../git/bioruby-samtools/lib/bio/db/sam/library.rb module Bio module DB module SAM module Library #IMPORTANT NOTE: Windows library is missing in this distribution # Return the path with the file name of the library for the specific operating system def filename #TODO refactor this piece of code in all the files lib_os = case RUBY_PLATFORM when /linux/ 'so.1' when /darwin/ 'dylib' when /windows/ 'dll' end File.join(File.expand_path(File.dirname(__FILE__)),'external',"libbam.#{lib_os}") end #filename module_function :filename end #Library end #Sam end #DB end #Bio ~/Downloads/git/bioruby-samtools$ rake test (in /home/mictadlo/Downloads/git/bioruby-samtools) /home/mictadlo/apps/ruby/bin/ruby -I"lib:lib:test" "/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in `block in ffi_lib': Could not open library '/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.so.1': /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.so.1: undefined symbol: bam_nt16_nt4_table (LoadError) from /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in `map' from /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in `ffi_lib' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:12:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:8:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:7:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:6:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:5:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `' from test/test_bio-samtools.rb:1:in `require' from test/test_bio-samtools.rb:1:in `' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `load' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `block in
' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `each' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `
' rake aborted! Command failed with status (1): [/home/mictadlo/apps/ruby/bin/ruby -I"lib:l...] /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:993:in `block in sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1027:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:115:in `block (2 levels) in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1110:in `verbose' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:100:in `block in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `block in execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:595:in `block in invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/monitor.rb:201:in `mon_synchronize' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:588:in `invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:581:in `invoke' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2041:in `invoke_task' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block (2 levels) in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2013:in `top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1992:in `run' /home/mictadlo/apps/ruby/bin/rake:31:in `
' ~/Downloads/git/bioruby-samtools$ ls /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/ libbam.a libbam.dylib libbam.so.1 What did I forget to do? Thank you in advance. Michal On 02/03/2011 08:10 PM, Tomoaki NISHIYAMA wrote: > Hi, > > As it says. > >> Run `bundle install` to install missing gems > > > $ bundle install > > will install all other required gems. > > The next thing to do is for the error: > > /home/tomoaki/ruby192p136/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in > `block in ffi_lib': Could not open library > '/home/tomoaki/bioruby-samtools/lib/bio/db/sam/external/libbam.a': > > Its natural that a dynamic library should be made for the purpose as > is in Mac OS X. > > $ make dylib > in the latest samtools and copy libbam.so.1 to > bioruby-samtools/lib/bio/db/sam/external/ > > > ------------CUT > diff --git a/lib/bio/db/sam/external/libbam.a > b/lib/bio/db/sam/external/libbam.a > index 0f231ef..aa1b225 100644 > Binary files a/lib/bio/db/sam/external/libbam.a and > b/lib/bio/db/sam/external/libbam.a differ > diff --git a/lib/bio/db/sam/library.rb b/lib/bio/db/sam/library.rb > index bb78515..e9f8b6e 100644 > --- a/lib/bio/db/sam/library.rb > +++ b/lib/bio/db/sam/library.rb > @@ -9,7 +9,7 @@ module Bio > #TODO refactor this piece of code in all the files > lib_os = case RUBY_PLATFORM > when /linux/ > - 'a' > + 'so.1' > when /darwin/ > 'dylib' > when /windows/ > @@ -22,4 +22,4 @@ module Bio > end #Library > end #Sam > end #DB > -end #Bio > \ No newline at end of file > +end #Bio > ------------CUT > > Then finally reached this state > > $ ~/ruby192p136/bin/rake > (in /home/tomoaki/bioruby-samtools) > /home/tomoaki/ruby192p136/bin/ruby -I"lib:lib:test" > "/home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader.rb" > "test/test_bio-samtools.rb" > Loaded suite > /home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader > Started > F > Finished in 0.000321 seconds. > > 1) Failure: > test: BioSamtools should probably rename this file and start testing > for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: > hey buddy, you should probably rename this file and start testing for > real > > Loading seems ok. > I'm not sure if this is bad or ok. > > Best regards From tomoakin at kenroku.kanazawa-u.ac.jp Fri Feb 4 03:31:22 2011 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Fri, 4 Feb 2011 17:31:22 +0900 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4BB255.7030703@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> Message-ID: Hi, > ~/Downloads/samtools-0.1.12a The *latest* samtools which I used was r910 via svn yesterday. r854 produced the same error as you have shown. Samtools is under very active development, as seen from the mailing list flow. So, some change in the samtools code made this difference, and its a bit difficult to keep track with all the update. -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan From bonnalraoul at ingm.it Fri Feb 4 05:33:05 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 4 Feb 2011 11:33:05 +0100 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4BB116.4010300@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <970B13D0-ADD4-478E-ABDB-6DBB7CD16DC7@ingm.it> <4D4BB116.4010300@gmail.com> Message-ID: <49287604-38A3-4058-A765-4B73F1B46A38@ingm.it> Thanks, please not that I found a problem using TopHat with samtools 0.1.12a I sent a mail to TopHat's developer but I didn't receive any answer yet. this is the original message : I'm Raoul a bioinformaticians, I'll start working on illumina data set in few days; in the mean time my group is doing tests. So, I have installed all the software, latest releases and today running my first alignment with tophat I got this error: [Fri Jan 28 10:43:20 2011] Checking for Samtools Traceback (most recent call last): File "/usr/local/bin/tophat", line 2223, in ? sys.exit(main()) File "/usr/local/bin/tophat", line 2136, in main check_samtools() File "/usr/local/bin/tophat", line 877, in check_samtools samtools_version = get_samtools_version() File "/usr/local/bin/tophat", line 864, in get_samtools_version samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')] ValueError: invalid literal for int(): 12a My samtools is Program: samtools (Tools for alignments in the SAM format) Version: 0.1.12a (r862) so i fixed the line #864 with import re samtools_version = [int(re.sub('[a-z]','',x.split('-')[0])) for x in version_val.split('.')] I know that it's quite ugly solution but .... I'm a ruby man :-) and I want to let you know that we, bioruby dev team, are putting a lot of effort to support your suite. Cheers. On 04/feb/2011, at 08.56, Michal wrote: > Please find attached the libbam.so.1 of samtools-0.1.12a. > > > On 02/03/2011 09:56 PM, Raoul Bonnal wrote: >> Thanks Tomoaki >> I missed the linux lib sorry, could you send me that library I'll add it to the repo. >> so.1 fixed >> >> On 03/feb/2011, at 11.10, Tomoaki NISHIYAMA wrote: >> >>> Hi, >>> >>> As it says. >>> >>>> Run `bundle install` to install missing gems >>> >>> $ bundle install >>> >>> will install all other required gems. >>> >>> The next thing to do is for the error: >>> >>> /home/tomoaki/ruby192p136/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in `block in ffi_lib': Could not open library '/home/tomoaki/bioruby-samtools/lib/bio/db/sam/external/libbam.a': >>> >>> Its natural that a dynamic library should be made for the purpose as is in Mac OS X. >>> >>> $ make dylib >>> in the latest samtools and copy libbam.so.1 to bioruby-samtools/lib/bio/db/sam/external/ >>> >>> >>> ------------CUT >>> diff --git a/lib/bio/db/sam/external/libbam.a b/lib/bio/db/sam/external/libbam.a >>> index 0f231ef..aa1b225 100644 >>> Binary files a/lib/bio/db/sam/external/libbam.a and b/lib/bio/db/sam/external/libbam.a differ >>> diff --git a/lib/bio/db/sam/library.rb b/lib/bio/db/sam/library.rb >>> index bb78515..e9f8b6e 100644 >>> --- a/lib/bio/db/sam/library.rb >>> +++ b/lib/bio/db/sam/library.rb >>> @@ -9,7 +9,7 @@ module Bio >>> #TODO refactor this piece of code in all the files >>> lib_os = case RUBY_PLATFORM >>> when /linux/ >>> - 'a' >>> + 'so.1' >>> when /darwin/ >>> 'dylib' >>> when /windows/ >>> @@ -22,4 +22,4 @@ module Bio >>> end #Library >>> end #Sam >>> end #DB >>> -end #Bio >>> \ No newline at end of file >>> +end #Bio >>> ------------CUT >>> >>> Then finally reached this state >>> >>> $ ~/ruby192p136/bin/rake >>> (in /home/tomoaki/bioruby-samtools) >>> /home/tomoaki/ruby192p136/bin/ruby -I"lib:lib:test" "/home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" >>> Loaded suite /home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader >>> Started >>> F >>> Finished in 0.000321 seconds. >>> >>> 1) Failure: >>> test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: >>> hey buddy, you should probably rename this file and start testing for real >>> >>> Loading seems ok. >>> I'm not sure if this is bad or ok. >>> >>> Best regards >>> -- >>> Tomoaki NISHIYAMA >>> >>> Advanced Science Research Center, >>> Kanazawa University, >>> 13-1 Takara-machi, >>> Kanazawa, 920-0934, Japan >>> >>> >>> On 2011/02/03, at 17:16, Michal wrote: >>> >>>> Dear Raoul, >>>> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: >>>> $ tar xvfz ruby-1.9.2-p136.tar.gz >>>> $ cd ruby-1.9.2-p136/ >>>> $ ./configure --prefix=/home/mictadlo/apps/ruby >>>> $ make >>>> $ make install >>>> $ vim ~/.bashrc >>>> export APPS=/home/mictadlo/apps >>>> export RUBY_HOME=$APPS/ruby >>>> export LD_LIBRARY_PATH=/RUBY_HOME/lib >>>> PATH=$RUBY_HOME/bin:$PATH >>>> $ . ~/.bashrc >>>> $ ruby -v >>>> ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] >>>> >>>> $ gem install ffi >>>> Building native extensions. This could take a while... >>>> Successfully installed ffi-1.0.5 >>>> 1 gem installed >>>> Installing ri documentation for ffi-1.0.5... >>>> Installing RDoc documentation for ffi-1.0.5... >>>> >>>> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git >>>> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ >>>> remote: Counting objects: 92, done. >>>> remote: Compressing objects: 100% (84/84), done. >>>> remote: Total 92 (delta 21), reused 0 (delta 0) >>>> Unpacking objects: 100% (92/92), done. >>>> >>>> ~/Downloads/git/bioruby-samtools$ rake test >>>> (in /home/mictadlo/Downloads/git/bioruby-samtools) >>>> rake aborted! >>>> no such file to load -- bundler >>>> :29:in `require' >>>> :29:in `require' >>>> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' >>>> /home/mictadlo/apps/ruby/bin/rake:31:in `
' >>>> >>>> What did I wrong? >>>> >>>> Thank you in advance. >>>> >>>> Michal >>>> >>>> On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >>>>> Dear Michal, >>>>> please check this out: >>>>> >>>>> https://github.com/helios/bioruby-samtools >>>>> >>>>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. >>>>> I need to test the linux library because I'm developing under osx. >>>>> If the libbam.a is wrong please give me the right one and I'll add it to the repo. >>>>> Also note that the library has been compiled for 64bit. >>>>> >>>>> Ciao! >>>>> >>>>> On 30/gen/2011, at 12.42, Michal wrote: >>>>> >>>>>> Hi, >>>>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >>>>>> >>>>>> What did I wrong? >>>>>> >>>>>> Michal >>>>>> _______________________________________________ >>>>>> BioRuby Project - http://www.bioruby.org/ >>>>>> BioRuby mailing list >>>>>> BioRuby at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>>> -- >>>>> R.J.P.B. >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >> -- >> R.J.P.B. >> >> >> >> >> > > -- R.J.P.B. From mictadlo at gmail.com Fri Feb 4 06:25:54 2011 From: mictadlo at gmail.com (Michal) Date: Fri, 04 Feb 2011 21:25:54 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> Message-ID: <4D4BE242.2030408@gmail.com> Hi, I have tried the svn version and I have got the following error: ~/Downloads/svn/ $ svn co https://samtools.svn.sourceforge.net/svnroot/samtools samtools Checked out revision 910. ~/Downloads/svn/samtools/trunk/samtools$ make dylib ~/Downloads/svn/samtools/trunk/samtools$ cp libbam.so.1 ~/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/ ~/Downloads/svn/samtools/trunk/samtools$ cd ~/Downloads/git/bioruby-samtools ~/Downloads/git/bioruby-samtools$ rake test (in /home/mictadlo/Downloads/git/bioruby-samtools) /home/mictadlo/apps/ruby/bin/ruby -I"lib:lib:test" "/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" Loaded suite /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader Started F Finished in 0.000371 seconds. 1) Failure: test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: hey buddy, you should probably rename this file and start testing for real 1 tests, 1 assertions, 1 failures, 0 errors, 0 skips Test run options: --seed 16981 rake aborted! Command failed with status (1): [/home/mictadlo/apps/ruby/bin/ruby -I"lib:l...] /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:993:in `block in sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1027:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:115:in `block (2 levels) in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1110:in `verbose' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:100:in `block in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `block in execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:595:in `block in invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/monitor.rb:201:in `mon_synchronize' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:588:in `invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:581:in `invoke' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2041:in `invoke_task' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block (2 levels) in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2013:in `top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1992:in `run' /home/mictadlo/apps/ruby/bin/rake:31:in `
' ~/Downloads/git/bioruby-samtools$ I understand how difficult it is to keep track and it is a good idea to ship bioruby-samtools with a working samtools version like Raoul does it. What I have forgotten to do? Thank you in advance. Michal On 02/04/2011 06:31 PM, Tomoaki NISHIYAMA wrote: > Hi, > >> ~/Downloads/samtools-0.1.12a > > The *latest* samtools which I used was r910 via svn yesterday. > r854 produced the same error as you have shown. > > Samtools is under very active development, as seen from the mailing > list flow. > So, some change in the samtools code made this difference, > and its a bit difficult to keep track with all the update. > > -- > > Tomoaki NISHIYAMA > > > Advanced Science Research Center, > > Kanazawa University, > > 13-1 Takara-machi, > > Kanazawa, 920-0934, Japan > > > From tomoakin at kenroku.kanazawa-u.ac.jp Fri Feb 4 07:26:24 2011 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Fri, 4 Feb 2011 21:26:24 +0900 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4BE242.2030408@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> <4D4BE242.2030408@gmail.com> Message-ID: Hi, > What I have forgotten to do? Now, you are at the point I reached yesterday and I don't think you have forgotten anything. From yesterday's mail: > 1) Failure: > test: BioSamtools should probably rename this file and start > testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: > hey buddy, you should probably rename this file and start testing > for real > > Loading seems ok. > I'm not sure if this is bad or ok. You could look at test/test_bio-samtools.rb $ cat test/test_bio-samtools.rb require 'helper' class TestBioSamtools < Test::Unit::TestCase should "probably rename this file and start testing for real" do flunk "hey buddy, you should probably rename this file and start testing for real" end end and guess what it means. My guess is that this is test not implemented yet. So, this error does not tell if the library function well or can not used at all. You might just try what you wanted to do and see if it works. > I understand how difficult it is to keep track and it is a good > idea to ship bioruby-samtools > with a working samtools version like Raoul does it. My view is the opposite. Since it potentially has many bugs and changes rapidly, bundled shipping is ineffective. With the lack of test code, we cannot even tell which is a good working version. -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan From mictadlo at gmail.com Fri Feb 4 08:13:33 2011 From: mictadlo at gmail.com (Michal) Date: Fri, 04 Feb 2011 23:13:33 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> <4D4BE242.2030408@gmail.com> Message-ID: <4D4BFB7D.9070004@gmail.com> Hi, I would be happy if would find out how to get on a particular position the alignment and then I could give feedback. Pysam http://code.google.com/p/pysam/ contains all files and tests. ~/Downloads/pysam-0.3.1/tests$ ls 00README.txt ex4.sam ex8.sam Makefile ex1.fa ex5.sam example.gtf.gz pysam_test.py ex1.sam.gz ex6.sam example.gtf.gz.tbi segfault_tests.py ex3.sam ex7.sam example.py tabix_test.py Maybe it would be possible to test bioruby-samtools in the same way. Pysam is ship out with samtools source code and maybe could be used it for bioruby-samtools. Thank you in advance. Michal On 02/04/2011 10:26 PM, Tomoaki NISHIYAMA wrote: > Hi, > >> What I have forgotten to do? > > Now, you are at the point I reached yesterday and > I don't think you have forgotten anything. > > From yesterday's mail: >> 1) Failure: >> test: BioSamtools should probably rename this file and start testing >> for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: >> hey buddy, you should probably rename this file and start testing for >> real >> >> Loading seems ok. >> I'm not sure if this is bad or ok. > > You could look at test/test_bio-samtools.rb > $ cat test/test_bio-samtools.rb > require 'helper' > > class TestBioSamtools < Test::Unit::TestCase > should "probably rename this file and start testing for real" do > flunk "hey buddy, you should probably rename this file and start > testing for real" > end > end > > and guess what it means. > > My guess is that this is test not implemented yet. > So, this error does not tell if the library function well or can not > used at all. > You might just try what you wanted to do and see if it works. > >> I understand how difficult it is to keep track and it is a good idea >> to ship bioruby-samtools >> with a working samtools version like Raoul does it. > > My view is the opposite. > Since it potentially has many bugs and changes rapidly, bundled > shipping is ineffective. > With the lack of test code, we cannot even tell which is a good > working version. > > -- > > Tomoaki NISHIYAMA > > > Advanced Science Research Center, > > Kanazawa University, > > 13-1 Takara-machi, > > Kanazawa, 920-0934, Japan > > From bonnalraoul at ingm.it Fri Feb 4 08:57:07 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 4 Feb 2011 14:57:07 +0100 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4BFB7D.9070004@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> <4D4BE242.2030408@gmail.com> <4D4BFB7D.9070004@gmail.com> Message-ID: <74EAEDFF-D8D0-42E0-93B8-51C4986CEC65@ingm.it> In these days, w.e. too, I have no time for sam tools. From the next week I could spend more time on this project and improve test, usability and platform supports. On 04/feb/2011, at 14.13, Michal wrote: > Hi, > I would be happy if would find out how to get on a particular position the alignment and then I could give feedback. > > Pysam http://code.google.com/p/pysam/ contains all files and tests. > ~/Downloads/pysam-0.3.1/tests$ ls > 00README.txt ex4.sam ex8.sam Makefile > ex1.fa ex5.sam example.gtf.gz pysam_test.py > ex1.sam.gz ex6.sam example.gtf.gz.tbi segfault_tests.py > ex3.sam ex7.sam example.py tabix_test.py > > Maybe it would be possible to test bioruby-samtools in the same way. Pysam is ship out with samtools source code and maybe could be used it for bioruby-samtools. > > Thank you in advance. > > Michal > > > On 02/04/2011 10:26 PM, Tomoaki NISHIYAMA wrote: >> >> Hi, >> >>> What I have forgotten to do? >> >> Now, you are at the point I reached yesterday and >> I don't think you have forgotten anything. >> >> From yesterday's mail: >>> 1) Failure: >>> test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: >>> hey buddy, you should probably rename this file and start testing for real >>> >>> Loading seems ok. >>> I'm not sure if this is bad or ok. >> >> You could look at test/test_bio-samtools.rb >> $ cat test/test_bio-samtools.rb >> require 'helper' >> >> class TestBioSamtools < Test::Unit::TestCase >> should "probably rename this file and start testing for real" do >> flunk "hey buddy, you should probably rename this file and start testing for real" >> end >> end >> >> and guess what it means. >> >> My guess is that this is test not implemented yet. >> So, this error does not tell if the library function well or can not used at all. >> You might just try what you wanted to do and see if it works. >> >>> I understand how difficult it is to keep track and it is a good idea to ship bioruby-samtools >>> with a working samtools version like Raoul does it. >> >> >> My view is the opposite. >> Since it potentially has many bugs and changes rapidly, bundled shipping is ineffective. >> With the lack of test code, we cannot even tell which is a good working version. >> -- >> Tomoaki NISHIYAMA >> >> Advanced Science Research Center, >> Kanazawa University, >> 13-1 Takara-machi, >> Kanazawa, 920-0934, Japan >> > -- R.J.P.B. From hlapp at drycafe.net Sat Feb 5 18:45:47 2011 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 5 Feb 2011 18:45:47 -0500 Subject: [BioRuby] NESCent Seeks Hackathon Whitepapers In-Reply-To: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> References: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> Message-ID: <066A2391-6041-408C-B26E-9B867DE785C7@drycafe.net> The National Evolutionary Synthesis Center (NESCent), in keeping with its objective to promote collaborative development of open-source, reusable, and standards-supporting informatics resources, sponsors highly collaborative, face-to-face software development events, called "hackathons" (see [1]). To ensure that this program continues to be responsive to user needs and to tap into the expertise and creativity of the evolutionary biology community, NESCent is soliciting short whitepapers (2-6 pages) [2] on potential target areas for future hackathons. To further encourage submissions, we have now distilled specific guidelines for proposing hackathon events, based on the experiences gained from events we have sponsored in the past: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines The Center's Call for Informatics Whitepapers [3] includes not only hackathons, but also a large spectrum of other initiatives to be undertaken by the Center, including training, software development, collaborative ontology development, and coordination of data standards. Whitepapers are accepted at any time and reviewed on an on- going basis. URLs: [1] Collaborative cyberinfrastructure events and programs organized by NESCent: http://informatics.nescent.org/wiki/Main_Page [2] NESCent Call for Informatics Whitepapers http://www.nescent.org/informatics/whitepapers.php [3] Hackathon Whitepaper Guidelines: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines [4] Past NESCent-sponsored hackathons: http://informatics.nescent.org/wiki/Main_Page#Hackathons From jan.aerts at gmail.com Mon Feb 7 03:42:24 2011 From: jan.aerts at gmail.com (Jan Aerts) Date: Mon, 7 Feb 2011 09:42:24 +0100 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> Message-ID: I've been using rake for my NGS analyses while I still worked at Sanger. Will post more about that in the next couple of days. jan. On 21 December 2010 18:50, Raoul Bonnal wrote: > My original request was on analysis approach on NGS and transcriptome. > > btw > > > Very interesting Hiro, > > searching on github there is also this project: > https://github.com/grosser/parallel > > Run any code in parallel Processes(> use all CPUs) or Threads(> speedup > blocking operations). > Best suited for map-reduce or e.g. parallel downloads/uploads. > Processes > > Speedup through multiple CPUs > Speedup for blocking operations > Protects global data > Extra memory used ( very low on REE through copy_on_write_friendly ) > Child processes are killed when your main process is killed through Ctrl+c > or kill -2 > Threads > > Speedup for blocking operations > Global data can be modified > No extra memory used > Processes/Threads are workers, they grab the next piece of work when they > finish > > > On 21/dic/2010, at 15.29, MISHIMA, Hiroyuki wrote: > > > Hi all, > > > > I would like to say something about workflow automation in Ruby. > > > > Recently I am interested in using Parallel Workflow extention for Rake > > (Pwrake) for NextGen sequencer data processing. As you may know, Rake is > Ruby Make, a build tool. > > > > Pwrake is developped by Masahiro Tanaka at University of Tsukuba. He is > > also the author of "NArray", very fast matrix calculation engine for > > Ruby. Although Pwrake and regular Rake are compatible in syntax, Pwrake > > automatically detects workflow steps that can be run in parallel. > > > > Pwrake's parallelization model is "process based". Because I am just a > > *user* of bioinformatics packages (like BWA/GATK/DINDEL etc..), it is > > what I need. > > > > Pwrake invokes processes via ssh and supports the Gfarm large-scale > > distributed filesystem. Of course, it works well on a multi-processor > > Linux box. > > > > Although Pwrake is developed for astronomy science, its goal is also > > common in bioinformatics. > > > > I think that some helper methods may simplify Rakefiles for > bioinformatics, and such helper methods are good for a BioRuby plugin. > > > > FYI, > > Pwrake on github: > > https://github.com/masa16/Pwrake/ > > > > Presentation at RubyConfX: > > http://www.slideshare.net/masa16tanaka/ruby-conftanaka16 > > > > Presentation at PRAGMA18: > > http://goc.pragma-grid.net/pragma-doc/pragma18/Cool_Things/pwrake.pptx > > > > Thanks, > > Hiro. > > > > Raoul Bonnal wrote(2010/12/21 21:33): > >> Hi all, I read in the irc's log that a lot of the memebers are or > >> will start working on ngs data. I'll re-start ( I worked on 454) with > >> the Illumina platform, in few week, do you have some consolidate > >> workflow to follow for transcriptome analysis ? > >> > >> papers, blogs, etc.. everything is ok :-) > >> > >> I'm also interested about the workflow discussion but... are the > >> workflow intended to let the not bioinformaticians analyze complex > >> datasets or automate some tedious and repetitive task that we > >> (bioinformaticians) must do every time ? In both cases our life will > >> be probably better :-) > >> > >> -- Ra > > -- > > MISHIMA, Hiroyuki, DDS, Ph.D. > > COE Research Fellow > > Department of Human Genetics > > Nagasaki University Graduate School of Biomedical Sciences > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From missy at be.to Mon Feb 7 07:32:34 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Mon, 07 Feb 2011 21:32:34 +0900 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> Message-ID: <4D4FE662.3070204@be.to> Hi Jan and all, I am looking forward to hearing from you about your experience on rake and NGS analyses. I have read your blog informative article ( http://saaientist.blogspot.com/ ) about rake for software projects and a GitHub repository BioRake ( https://github.com/jandot/biorake ). BioRake's "event" method is elegant. In my DINDEL workflow rakefile, I use a dummy file as a representative of all dynamically generated intermediate files in Stage 3. The event method may express the logic and simplify the description. Sincerely yours, Hiro. Jan Aerts wrote (2011/02/07 17:42): > I've been using rake for my NGS analyses while I still worked at > Sanger. Will post more about that in the next couple of days. > > jan. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From pjotr.public14 at thebird.nl Mon Feb 7 12:16:55 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 7 Feb 2011 18:16:55 +0100 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> Message-ID: <20110207171655.GA25517@thebird.nl> On Mon, Feb 07, 2011 at 09:42:24AM +0100, Jan Aerts wrote: > I've been using rake for my NGS analyses while I still worked at Sanger. > Will post more about that in the next couple of days. It is interesting to integrate it with rq - which can parallelize calculations with zero-administration (all that is needed is a shared dir). I kinda 'inherited' the project, and introduced a few bugs, see https://github.com/pjotrp/rq It will soon have a debian package. Pj. From missy at be.to Mon Feb 7 20:06:57 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Tue, 08 Feb 2011 10:06:57 +0900 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: <20110207171655.GA25517@thebird.nl> References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> <20110207171655.GA25517@thebird.nl> Message-ID: <4D509731.4050209@be.to> Hi, I added Pjotr's information on the BioRuby wiki ( http://bioruby.open-bio.org/wiki/Workflows ). I also updated a subsection about GridEngine. Univa took over GridEngine development from Oracle. Sincerely yours, Hiro. Pjotr Prins wrote (2011/02/08 2:16): > rq - which can parallelize calculations with zero-administration > (all that is needed is a shared dir). -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From bonnalraoul at ingm.it Wed Feb 9 06:58:50 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 9 Feb 2011 12:58:50 +0100 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: <4D509731.4050209@be.to> References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> <20110207171655.GA25517@thebird.nl> <4D509731.4050209@be.to> Message-ID: <97CFB702-337B-4608-8AF5-CADAB7B1702A@ingm.it> Hello folks, tweeting around I found these videos http://www.youtube.com/watch?v=1ntxT-47VPA http://www.youtube.com/watch?v=OpaiGYxkSuQ&feature=related http://www.youtube.com/watch?v=P40akGWJ_gY&feature=related Project home page: http://www.gnu.org/software/parallel/ Very useful in many contexts. @BioRuby: I think that we can explore how to use it in workflows. On 08/feb/2011, at 02.06, MISHIMA, Hiroyuki wrote: > Hi, > > I added Pjotr's information on the BioRuby wiki > ( http://bioruby.open-bio.org/wiki/Workflows ). > > I also updated a subsection about GridEngine. Univa took over GridEngine > development from Oracle. > > Sincerely yours, > Hiro. > > Pjotr Prins wrote (2011/02/08 2:16): >> rq - which can parallelize calculations with zero-administration >> (all that is needed is a shared dir). > > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra From francesco.strozzi at gmail.com Wed Feb 9 08:13:00 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Wed, 9 Feb 2011 14:13:00 +0100 Subject: [BioRuby] Bio::BWA Message-ID: Hi all, the version 0.1 of the BWA Plugin is now available for tests! The code is at https://github.com/fstrozzi/bioruby-bwa Details on this plugin with some examples are available at https://github.com/fstrozzi/bioruby-bwa/wiki Plugin documentation is available at http://fstrozzi.github.com/bioruby-bwa/ The plugin runs with ruby-ffi and includes two pre-compiled BWA shared libraries for Linux and Mac OS X (64bit only). I've run tests on both systems and the results are fine. For what I have seen the plugin works with the same performance as the standalone BWA (I will add details on the benchmarks to the wiki asap). Before releasing a gem I would like more tests from someone else other than me ;-). Particularly to check if the pre-compiled libraries works fine or if there are issues here and there. So please checkout the code, try it and let me know your feedbacks! Thanks and cheers -- Francesco From missy at be.to Wed Feb 9 23:59:42 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Thu, 10 Feb 2011 13:59:42 +0900 Subject: [BioRuby] Spamming on the BioRuby wiki Message-ID: <4D5370BE.3050407@be.to> Hi, Recently, I found spamming on the BioRuby wiki. Many user accounts and spam articles seem to be created automatically. Does anyone know good ways to prevent such activities? Sincerely yours, Hiro -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From ktym at hgc.jp Thu Feb 10 00:32:53 2011 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu, 10 Feb 2011 14:32:53 +0900 Subject: [BioRuby] Spamming on the BioRuby wiki In-Reply-To: <4D5370BE.3050407@be.to> References: <4D5370BE.3050407@be.to> Message-ID: Hi Hiro, Thank you for your notification and deletion of spam texts. We had a similar problem few months ago but it occurred again, very sad. We don't want to waste our time for reverting those wiki pages anymore, I'll ask OBF staff to require authorization before creating new account. Judged from current usage of the wiki and the size of our community, I think this change won't spoil our activity. Toshiaki On 2011/02/10, at 13:59, MISHIMA, Hiroyuki wrote: > Hi, > > Recently, I found spamming on the BioRuby wiki. Many user accounts and > spam articles seem to be created automatically. > > Does anyone know good ways to prevent such activities? > > Sincerely yours, > Hiro > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From cjfields at illinois.edu Thu Feb 10 09:26:52 2011 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 10 Feb 2011 08:26:52 -0600 Subject: [BioRuby] Spamming on the BioRuby wiki In-Reply-To: References: <4D5370BE.3050407@be.to> Message-ID: <2820FD5F-A103-480C-9E78-BD172A7F169E@illinois.edu> This has been happening across all the OBF wikis unfortunately. I think Jason is adding a ReCaptcha system for bioperl.org, might be a good idea to do the same for bioruby. chris On Feb 9, 2011, at 11:32 PM, Toshiaki Katayama wrote: > Hi Hiro, > > Thank you for your notification and deletion of spam texts. > We had a similar problem few months ago but it occurred again, very sad. > > We don't want to waste our time for reverting those wiki pages anymore, > I'll ask OBF staff to require authorization before creating new account. > Judged from current usage of the wiki and the size of our community, > I think this change won't spoil our activity. > > Toshiaki > > > On 2011/02/10, at 13:59, MISHIMA, Hiroyuki wrote: > >> Hi, >> >> Recently, I found spamming on the BioRuby wiki. Many user accounts and >> spam articles seem to be created automatically. >> >> Does anyone know good ways to prevent such activities? >> >> Sincerely yours, >> Hiro >> -- >> MISHIMA, Hiroyuki, DDS, Ph.D. >> COE Research Fellow >> Department of Human Genetics >> Nagasaki University Graduate School of Biomedical Sciences >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From mikeco57 at gmail.com Thu Feb 10 13:29:07 2011 From: mikeco57 at gmail.com (Michael O'Keefe) Date: Thu, 10 Feb 2011 13:29:07 -0500 Subject: [BioRuby] Contributing Message-ID: <4D542E73.5060708@gmail.com> Hello everyone, My name is Michael O'Keefe. I am a student in bioinformatics at Rensselaer Polytechnic Institute, and I am participating in a group that sponsors work on open-source projects ( rcos.cs.rpi.edu ). I would like to contribute to BioRuby, and would like to know where the best place to start is. Is there a specific part of the project that I could work on? I wouldn't mind working on bugfixes, or any other project that could use some work. Thank you very much, Michael O'Keefe mikeco57 at gmail.com From p.j.a.cock at googlemail.com Fri Feb 11 19:12:06 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 12 Feb 2011 00:12:06 +0000 Subject: [BioRuby] Spamming on the BioRuby wiki In-Reply-To: <2820FD5F-A103-480C-9E78-BD172A7F169E@illinois.edu> References: <4D5370BE.3050407@be.to> <2820FD5F-A103-480C-9E78-BD172A7F169E@illinois.edu> Message-ID: On Thu, Feb 10, 2011 at 2:26 PM, Chris Fields wrote: > This has been happening across all the OBF wikis unfortunately. >?I think Jason is adding a ReCaptcha system for bioperl.org, > might be a good idea to do the same for bioruby. > > chris Hi Chris, I hope the ReCaptcha system works and can be applied to all the OBF wikis. If it doesn't stop the spam, I think the suggestion that account creation should require manual authorisation is a good idea - certainly on Biopython the number of real wiki account requests is low. Peter From cjfields at illinois.edu Fri Feb 11 20:29:59 2011 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 11 Feb 2011 19:29:59 -0600 Subject: [BioRuby] Spamming on the BioRuby wiki In-Reply-To: References: <4D5370BE.3050407@be.to> <2820FD5F-A103-480C-9E78-BD172A7F169E@illinois.edu> Message-ID: <740EE9EF-458F-45BF-B8AF-641CAC292BB7@illinois.edu> On Feb 11, 2011, at 6:12 PM, Peter Cock wrote: > On Thu, Feb 10, 2011 at 2:26 PM, Chris Fields wrote: >> This has been happening across all the OBF wikis unfortunately. >> I think Jason is adding a ReCaptcha system for bioperl.org, >> might be a good idea to do the same for bioruby. >> >> chris > > Hi Chris, > > I hope the ReCaptcha system works and can be applied > to all the OBF wikis. If it doesn't stop the spam, I think > the suggestion that account creation should require manual > authorisation is a good idea - certainly on Biopython the > number of real wiki account requests is low. > > Peter We can switch to that if needed. Jason had problems getting ReCaptcha working, but I may take a crack at it before we move to a manual system (which may be more of a pain, considering how many spam requests might be made). chris From pjotr.public14 at thebird.nl Mon Feb 14 09:46:39 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 14 Feb 2011 15:46:39 +0100 Subject: [BioRuby] Plugins, Biogem and Christmas 2010 In-Reply-To: <3F1D10FB-B121-4819-A519-87A6637DD8F6@ingm.it> References: <3F1D10FB-B121-4819-A519-87A6637DD8F6@ingm.it> Message-ID: <20110214144639.GA26838@thebird.nl> Yet another BioRuby plugin. I just released a fast BLAST XML file parser for big data (i.e. it does not necessarily load everything in memory). It is based on Nokogiri+libxml2. A quick test shows it is 50x faster than the ReXML parser that comes with BioRuby. Install with gem install bio-blastxmlparse It comes with a utility to produce tabular output blastxmlparser --help Docs at https://github.com/pjotrp/blastxmlparser (you may need to install libxml2-dev first, to build the native extension). There is a choice of two parsers, loading the DOM in memory, or split the XML file in smaller sections. I ran quite a few test to see what type of parsing would give best results. Currently I parse the DOM, walk the low level nodes, and use (lazy) XPath for the values. There is probably still room for improvement. One thing I will still try, when I have time, is parallelized parsing on JRuby. With that it should be one of the fastest BLAST parsers on the planet. Enjoy, Pj. On Fri, Dec 24, 2010 at 12:08:04PM +0100, Raoul Bonnal wrote: > BioRuby plugin system was firstly announced at [BOSC 2010] and will be implemented by the Christmas 2010. Hopefully. :) -- Yes, we made it! Check out the BiogemInstallation and BiogemDevelopment sections. From pjotr.public14 at thebird.nl Tue Feb 15 03:14:57 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 15 Feb 2011 09:14:57 +0100 Subject: [BioRuby] Plugins, Biogem and Christmas 2010 In-Reply-To: <20110214144639.GA26838@thebird.nl> References: <3F1D10FB-B121-4819-A519-87A6637DD8F6@ingm.it> <20110214144639.GA26838@thebird.nl> Message-ID: <20110215081457.GA30678@thebird.nl> At this point bio-blastxmlparse works on Ruby 1.9 only. It should be possible to use Enumerator on 1.8 - I'll look into that at some point. Pj. From bonnalraoul at ingm.it Tue Feb 15 04:37:36 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Tue, 15 Feb 2011 10:37:36 +0100 Subject: [BioRuby] SRA downloader Message-ID: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> Hey Guys, this is a new plugin to download sra archives in an easy way, I hope :-) Why ? because I need to download some file from SRA and I don't want to type the wget/curl command and I want to explore the ftp from command line, then because I need to start the downloads in background on a remote server. Where ? https://github.com/helios/bioruby-sradl as usual is experimental so, please be careful. I'm quite lazy so test section doesn't exist and the code needs some refactoring; I know I'll add it soon. The DSL needs to be improved. The procedure is recursive so you can download a bunch of reads at the same time. By default the reads downloaded are the LITE. In the read me there is an example of looking for a regular archive: it's also an example of using optional parameters in thor' scripts. To post process SRA format you need the sra tools kit http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.3_Installing_the_Too This plugin has also the purpose to be demonstrative for a Thor application. This could be added to our NGS ngs section. Any suggestion is welcome. Ciao. -- Ra From bonnalraoul at ingm.it Tue Feb 15 05:25:26 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Tue, 15 Feb 2011 11:25:26 +0100 Subject: [BioRuby] SRA downloader In-Reply-To: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> Message-ID: <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> Next time a little bit of research :-( http://phylogenomics.blogspot.com/2011/02/though-i-generally-love-ncbi.html?showComment=1297359206321#c7246439301219289057 On 15/feb/2011, at 10.37, Raoul Bonnal wrote: > Hey Guys, > this is a new plugin to download sra archives in an easy way, I hope :-) > > Why ? because I need to download some file from SRA and I don't want to type the wget/curl command and I want to explore the ftp from command line, then because I need to start the downloads in background on a remote server. > > Where ? https://github.com/helios/bioruby-sradl > > as usual is experimental so, please be careful. I'm quite lazy so test section doesn't exist and the code needs some refactoring; I know I'll add it soon. > The DSL needs to be improved. > > The procedure is recursive so you can download a bunch of reads at the same time. > > By default the reads downloaded are the LITE. In the read me there is an example of looking for a regular archive: it's also an example of using optional parameters in thor' scripts. > To post process SRA format you need the sra tools kit > > http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.3_Installing_the_Too > > This plugin has also the purpose to be demonstrative for a Thor application. > > This could be added to our NGS ngs section. > > Any suggestion is welcome. > > Ciao. > -- > Ra > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra From p.j.a.cock at googlemail.com Tue Feb 15 08:18:47 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 15 Feb 2011 13:18:47 +0000 Subject: [BioRuby] SRA downloader In-Reply-To: <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> Message-ID: On Tue, Feb 15, 2011 at 10:25 AM, Raoul Bonnal wrote: > Next time a little bit of research ?:-( > > http://phylogenomics.blogspot.com/2011/02/though-i-generally-love-ncbi.html?showComment=1297359206321#c7246439301219289057 > Still no official announcement yet though... > On 15/feb/2011, at 10.37, Raoul Bonnal wrote: > >> Hey Guys, >> this is a new plugin to download sra archives in an easy way, I hope :-) >> >> Why ? because I need to download some file from SRA and I don't want >> to type the wget/curl command and I want to explore the ftp from command >> line, then because I need to start the downloads in background on a remote >> server. >> You might be interested in this solution too, http://fungalgenomes.org/blog/2011/02/a-hyphaltip-get-a-bunch-of-sra-data/ Peter From bonnalraoul at ingm.it Tue Feb 15 08:45:09 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Tue, 15 Feb 2011 14:45:09 +0100 Subject: [BioRuby] SRA downloader In-Reply-To: References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> Message-ID: <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> Hi Peter, On 15/feb/2011, at 14.18, Peter Cock wrote: > http://fungalgenomes.org/blog/2011/02/a-hyphaltip-get-a-bunch-of-sra-data/ thanks for the link. Actually, DDBJ and EBI (ENA) have a repository for SRA datasets. The question is? Do we need to support SRA or it's just a convenient way for providers to store data? EBI seems to me more computer friendly than NIH site. If more providers will switch to Aspera, there is a developer kit SDK http://www.asperasoft.com/en/products/fasp_SDK_9/fasp_SDK_9 that could be interesting to support. Today I tested the download speed and it performs very well compared to normal ftp. -- Ra From cjfields at illinois.edu Tue Feb 15 09:57:17 2011 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 15 Feb 2011 08:57:17 -0600 Subject: [BioRuby] SRA downloader In-Reply-To: <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> Message-ID: <62BA7169-FB1F-42E6-AD8B-16BEC9E356E4@illinois.edu> On Feb 15, 2011, at 7:45 AM, Raoul Bonnal wrote: > Hi Peter, > On 15/feb/2011, at 14.18, Peter Cock wrote: > >> http://fungalgenomes.org/blog/2011/02/a-hyphaltip-get-a-bunch-of-sra-data/ > thanks for the link. > > Actually, DDBJ and EBI (ENA) have a repository for SRA datasets. > The question is? Do we need to support SRA or it's just a convenient way for providers to store data? Yes, I think there needs to be support for easier data retrieval, but of course only if there will be a SRA database to being with. All the feedback (both positive and negative) from Eisen's blog indicates the need for such a resource, albeit with an improved UI. Unfortunately, the most significant problem we're seeing on the NCBI end is (I believe) a general lack of funding for on-going and new projects; this has been going on for a while now. As Peter pointed out removal of SRA and other resources hasn't been made official (the link quotes an anonymous source). However, past cuts at NCBI and the newly released federal budget doesn't make me think there will be a stop gap to prevent SRA and other NCBI resources from going away. > EBI seems to me more computer friendly than NIH site. I generally find the same. > If more providers will switch to Aspera, there is a developer kit SDK http://www.asperasoft.com/en/products/fasp_SDK_9/fasp_SDK_9 that could be interesting to support. > > Today I tested the download speed and it performs very well compared to normal ftp. > > -- > Ra A bit confused on this last part. If we're talking about a simple ftp-like resource to pull data from then I would suggest biotorrents, which is specifically developed for handling large datasets. However, a gzipped blob with an accession is useless without a way to add additional meta-information about it (species, source, protocols, etc etc) and a way to search through such information. Most users will want a searchable and possibly curated repository to pull data from, or at least one that gives them accessions and links to such. There is a need for something like SRA whether NCBI or others decide to handle it. chris From francesco.strozzi at gmail.com Tue Feb 15 11:09:36 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Tue, 15 Feb 2011 17:09:36 +0100 Subject: [BioRuby] bioruby sff reader Message-ID: Hi all, is there a SFF reader to parse 454 output in Ruby? Or is someone working on this? It will be nice to have something like python sff-extract which can read the SFF format and generate ad hoc files like FastQ or Fasta, Qual and XML traceinfo. Bye -- Francesco From p.j.a.cock at googlemail.com Tue Feb 15 11:53:03 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 15 Feb 2011 16:53:03 +0000 Subject: [BioRuby] bioruby sff reader In-Reply-To: References: Message-ID: On Tue, Feb 15, 2011 at 4:09 PM, Francesco Strozzi wrote: > Hi all, > is there a SFF reader to parse 454 output in Ruby? Or is someone working on > this? > It will be nice to have something like python sff-extract which can read the > SFF format and generate ad hoc files like FastQ or Fasta, Qual and XML > traceinfo. If all you want to to convert SFF to FASTQ or FASTA+QUAL plus perhaps the NCBI XML traceinfo why not just use the sff_extract.py script? On the other hand, I can see the utlity in native support for SFF files in (Bio)Ruby. Biopython does this already and there has been some work towards this for BioPerl and BioJava too: http://lists.open-bio.org/pipermail/bioperl-l/2010-November/034223.html http://lists.open-bio.org/pipermail/biojava-dev/2010-November/004451.html Please feel free to look at the Biopython SFF code for this. It was originally based on sff_extract for parsing, but extended to also write SFF and handle the (undocumented) Roche index block. I've tried to include enough comments within the code to make it clear, but I'll happily answer technical questions: https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py There are also unit test example files you can use: https://github.com/biopython/biopython/tree/master/Tests/Roche Peter (Biopython) From bonnalraoul at ingm.it Wed Feb 16 05:31:05 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 16 Feb 2011 11:31:05 +0100 Subject: [BioRuby] Contributing In-Reply-To: <4D542E73.5060708@gmail.com> References: <4D542E73.5060708@gmail.com> Message-ID: <3D975070-639D-475C-8DB2-770A3573793D@ingm.it> Dear Michael, thanks for your interest. Why not to join our regular irc meeting tomorrow (CEST time around 15:00) on irc.freenode.net channel #bioruby ? I'm Helius or ilpuccio on chat. Now, we are working on different topics like workflows, ngs and plugins, you are welcome to contribute in any on them. Now I'm here with Francesco and we think that as a new "biorubyer" it would be very useful if you take a look at the tutorial section and verify is there is something that needs improvements or you miss as a beginner. http://bioruby.open-bio.org/wiki/Tutorial In which field of bioinformatics are you working ? PS: Busy days, delay's reason, sorry. On 10/feb/2011, at 19.29, Michael O'Keefe wrote: > Hello everyone, > > My name is Michael O'Keefe. I am a student in bioinformatics at Rensselaer Polytechnic Institute, and I am participating in a group that sponsors work on open-source projects ( rcos.cs.rpi.edu ). I would like to contribute to BioRuby, and would like to know where the best place to start is. Is there a specific part of the project that I could work on? I wouldn't mind working on bugfixes, or any other project that could use some work. > > Thank you very much, > Michael O'Keefe > mikeco57 at gmail.com > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby Ciao. -- Ra From bonnalraoul at ingm.it Fri Feb 18 06:14:47 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 18 Feb 2011 12:14:47 +0100 Subject: [BioRuby] SRA downloader In-Reply-To: <62BA7169-FB1F-42E6-AD8B-16BEC9E356E4@illinois.edu> References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> <62BA7169-FB1F-42E6-AD8B-16BEC9E356E4@illinois.edu> Message-ID: Hi Chris, On 15/feb/2011, at 15.57, Chris Fields wrote: > On Feb 15, 2011, at 7:45 AM, Raoul Bonnal wrote: > >> If more providers will switch to Aspera, there is a developer kit SDK http://www.asperasoft.com/en/products/fasp_SDK_9/fasp_SDK_9 that could be interesting to support. >> >> Today I tested the download speed and it performs very well compared to normal ftp. >> >> -- >> Ra > > A bit confused on this last part. If we're talking about a simple ftp-like resource to pull data from then I would suggest biotorrents, which is specifically developed for handling large datasets. My point was, NCBI and EBI use Aspera, which has a proprietary way to transfer file, you need their client for a fast download... but don't care about that I don't like that approach. Why are they not using torrents ? Which is the sense of biotorrent ? Just share "personal" data or replicate/mirroring other databases ? I must admit that I need just some SRA file for testing tools. I don't think I will download many sra data in the near future, I can wait 50mins using regular ftp. It was more, which is your feeling with sra and your experience. -- Ra From mh6 at sanger.ac.uk Fri Feb 18 06:38:56 2011 From: mh6 at sanger.ac.uk (Michael Paulini) Date: Fri, 18 Feb 2011 11:38:56 +0000 Subject: [BioRuby] SRA downloader In-Reply-To: References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> <62BA7169-FB1F-42E6-AD8B-16BEC9E356E4@illinois.edu> Message-ID: <4D5E5A50.1000200@sanger.ac.uk> On 18/02/2011 11:14, Raoul Bonnal wrote: > Hi Chris, > > On 15/feb/2011, at 15.57, Chris Fields wrote: > >> On Feb 15, 2011, at 7:45 AM, Raoul Bonnal wrote: >> >>> If more providers will switch to Aspera, there is a developer kit SDK http://www.asperasoft.com/en/products/fasp_SDK_9/fasp_SDK_9 that could be interesting to support. >>> >>> Today I tested the download speed and it performs very well compared to normal ftp. >>> >>> -- >>> Ra >> A bit confused on this last part. If we're talking about a simple ftp-like resource to pull data from then I would suggest biotorrents, which is specifically developed for handling large datasets. > My point was, NCBI and EBI use Aspera, which has a proprietary way to transfer file, you need their client for a fast download... but don't care about that I don't like that approach. > > Why are they not using torrents ? Which is the sense of biotorrent ? Just share "personal" data or replicate/mirroring other databases ? > > I must admit that I need just some SRA file for testing tools. I don't think I will download many sra data in the near future, I can wait 50mins using regular ftp. > > It was more, which is your feeling with sra and your experience. > > -- > Ra > Hi Ra, from personal experience the word 'bittorrent' does not fly too high with management ... even if used to distributed 20GB+ VM images. After long-winded fights (making sure we were allowed to distribute every single file, by attaching the respective OSS license to them, and getting agreements form our sister sites to seed), we went back to mirror them across a handful FTP sites instead, as it was "decided" that we can't possible use 'File-Sharing Programs'. M /rant_end -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From mail at michaelbarton.me.uk Mon Feb 21 12:06:07 2011 From: mail at michaelbarton.me.uk (Michael Barton) Date: Mon, 21 Feb 2011 12:06:07 -0500 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension Message-ID: <20110221170607.GA14295@Michael-Bartons-MacBook.local> Hi, Does anyone know of a ruby library for doing local and global sequence alignment? I'm interested in performing these kind of alignments in ruby but would prefer not to call command line tools such as EMBOSS. I think it could be useful to have a ruby gem which installs a C-extension for allowing for reasonably fast alignment. A cursory look on pubmed turned these links for C libraries. http://www.ncbi.nlm.nih.gov/pubmed/18959793 http://www.ncbi.nlm.nih.gov/books/NBK7151/ Mike From francesco.strozzi at gmail.com Tue Feb 22 03:58:12 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Tue, 22 Feb 2011 09:58:12 +0100 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110221170607.GA14295@Michael-Bartons-MacBook.local> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> Message-ID: Hi Michael, I have worked on a Ruby binding to the BWA fast mapping software using FFI. With BWA you can run global alignments as well as local alignments with the standard SW algorithm included in BWA. This is not released as a gem yet, as it's still under testing. If you want to check it out and see if it fits for your purpose you can find the code here : https://github.com/fstrozzi/bioruby-bwa The package includes two pre-compiled libraries for Mac OS X and Linux (64bit only). Cheers Francesco On Mon, Feb 21, 2011 at 18:06, Michael Barton wrote: > Hi, > > Does anyone know of a ruby library for doing local and global sequence > alignment? I'm interested in performing these kind of alignments in ruby > but > would prefer not to call command line tools such as EMBOSS. I think it > could be > useful to have a ruby gem which installs a C-extension for allowing for > reasonably fast alignment. A cursory look on pubmed turned these links for > C libraries. > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > Mike > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > -- Francesco From ngoto at gen-info.osaka-u.ac.jp Tue Feb 22 04:11:20 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 22 Feb 2011 18:11:20 +0900 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110221170607.GA14295@Michael-Bartons-MacBook.local> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> Message-ID: <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> Hi, There was SWlib, an implementation of Smith-Waterman algorithm for Ruby. It was written by OKUJI K. Yoshinori in 2001. Since it is very old, some modification would be needed for correct working. http://bioruby.open-bio.org/contrib/swlib/ Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Mon, 21 Feb 2011 12:06:07 -0500 Michael Barton wrote: > Hi, > > Does anyone know of a ruby library for doing local and global sequence > alignment? I'm interested in performing these kind of alignments in ruby but > would prefer not to call command line tools such as EMBOSS. I think it could be > useful to have a ruby gem which installs a C-extension for allowing for > reasonably fast alignment. A cursory look on pubmed turned these links for > C libraries. > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > Mike From mail at michaelbarton.me.uk Tue Feb 22 11:48:21 2011 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 22 Feb 2011 11:48:21 -0500 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20110222164821.GA2096@nku069218.hh.nku.edu> Thank you Naohisa and Francesco for your suggestions. I will try experimenting with these two libraries. I had also just read an interesting article on using C extensions in Ruby which I thought might be of general interest to the mailing list - http://robots.thoughtbot.com/post/1037240922 On Tue, Feb 22, 2011 at 06:11:20PM +0900, Naohisa GOTO wrote: > Hi, > > There was SWlib, an implementation of Smith-Waterman algorithm for Ruby. It > was written by OKUJI K. Yoshinori in 2001. Since it is very old, some > modification would be needed for correct working. > http://bioruby.open-bio.org/contrib/swlib/ > > Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > On Mon, 21 Feb 2011 12:06:07 -0500 Michael Barton > wrote: > > > Hi, > > > > Does anyone know of a ruby library for doing local and global sequence > > alignment? I'm interested in performing these kind of alignments in ruby > > but would prefer not to call command line tools such as EMBOSS. I think it > > could be useful to have a ruby gem which installs a C-extension for > > allowing for reasonably fast alignment. A cursory look on pubmed turned > > these links for C libraries. > > > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > > > Mike > > _______________________________________________ BioRuby Project > - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnalraoul at ingm.it Tue Feb 22 13:36:36 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Tue, 22 Feb 2011 19:36:36 +0100 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222164821.GA2096@nku069218.hh.nku.edu> Message-ID: <20110222183636.8da2b75f@mail.ingm.it> Hi Michael, thanks for the post. Why not open a Geek section on the wiki for this type of links ? _____ From: Michael Barton [mailto:mail at michaelbarton.me.uk] To: BioRuby Mailing List [mailto:bioruby at lists.open-bio.org] Sent: Tue, 22 Feb 2011 17:48:21 +0100 Subject: Re: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension Thank you Naohisa and Francesco for your suggestions. I will try experimenting with these two libraries. I had also just read an interesting article on using C extensions in Ruby which I thought might be of general interest to the mailing list - http://robots.thoughtbot.com/post/1037240922 On Tue, Feb 22, 2011 at 06:11:20PM +0900, Naohisa GOTO wrote: > Hi, > > There was SWlib, an implementation of Smith-Waterman algorithm for Ruby. It > was written by OKUJI K. Yoshinori in 2001. Since it is very old, some > modification would be needed for correct working. > http://bioruby.open-bio.org/contrib/swlib/ > > Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > On Mon, 21 Feb 2011 12:06:07 -0500 Michael Barton > wrote: > > > Hi, > > > > Does anyone know of a ruby library for doing local and global sequence > > alignment? I'm interested in performing these kind of alignments in ruby > > but would prefer not to call command line tools such as EMBOSS. I think it > > could be useful to have a ruby gem which installs a C-extension for > > allowing for reasonably fast alignment. A cursory look on pubmed turned > > these links for C libraries. > > > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > > > Mike > > _______________________________________________ BioRuby Project > - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Tue Feb 22 13:47:41 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 22 Feb 2011 19:47:41 +0100 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222164821.GA2096@nku069218.hh.nku.edu> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> <20110222164821.GA2096@nku069218.hh.nku.edu> Message-ID: <20110222184741.GA21681@thebird.nl> On Tue, Feb 22, 2011 at 11:48:21AM -0500, Michael Barton wrote: > Thank you Naohisa and Francesco for your suggestions. I will try experimenting > with these two libraries. I had also just read an interesting article on using > C extensions in Ruby which I thought might be of general interest to the > mailing list - > > http://robots.thoughtbot.com/post/1037240922 This discusses using a Ruby C interface. Note: it is not the easiest way. Especially with existing C libs you may be better off with FFI or SWIG. The first makes mapping to Ruby easy, the second maps to all languages. For most Ruby bindings FFI is preferred, also because it does JRuby. Binding existing libraries is usually non-trivial. Because C has no GC, and buffers get passed around as function parameters. Pj. From mail at michaelbarton.me.uk Tue Feb 22 14:43:09 2011 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 22 Feb 2011 14:43:09 -0500 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222184741.GA21681@thebird.nl> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> <20110222164821.GA2096@nku069218.hh.nku.edu> <20110222184741.GA21681@thebird.nl> Message-ID: <20110222194309.GB5855@nku069218.hh.nku.edu> That's useful to know. I was familiar with FFI but I didn't know it was the preferred approach in Ruby. I'm learning C and hoping to use it where necessary for solving bottle necks. On Tue, Feb 22, 2011 at 07:47:41PM +0100, Pjotr Prins wrote: > On Tue, Feb 22, 2011 at 11:48:21AM -0500, Michael Barton wrote: > > Thank you Naohisa and Francesco for your suggestions. I will try > > experimenting with these two libraries. I had also just read an interesting > > article on using C extensions in Ruby which I thought might be of general > > interest to the mailing list - > > > > http://robots.thoughtbot.com/post/1037240922 > > This discusses using a Ruby C interface. Note: it is not the easiest way. > Especially with existing C libs you may be better off with FFI or SWIG. The > first makes mapping to Ruby easy, the second maps to all languages. For most > Ruby bindings FFI is preferred, also because it does JRuby. > > Binding existing libraries is usually non-trivial. Because C has no GC, and > buffers get passed around as function parameters. > > Pj. From mail at michaelbarton.me.uk Tue Feb 22 14:59:17 2011 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 22 Feb 2011 14:59:17 -0500 Subject: [BioRuby] BioRuby interesting links and documentation. In-Reply-To: <20110222183636.8da2b75f@mail.ingm.it> References: <20110222164821.GA2096@nku069218.hh.nku.edu> <20110222183636.8da2b75f@mail.ingm.it> Message-ID: <20110222195917.GA5949@nku069218.hh.nku.edu> I thought I should reply to Raoul's email with a different topic name. One way could be to share interesting links through some sort of feed? A community blog or twitter? I think the wiki needs some attention in places, e.g. the sample codes page has many headings with "TBD" as the content. The doc rails project seems to have been quite successful for the Rails community. Rather than a wiki it's a static site on github. I think the reason of it's success is that one person is responsible for it (@pratiknaik). On Tue, Feb 22, 2011 at 07:36:36PM +0100, Raoul Bonnal wrote: > Hi Michael, thanks for the post. Why not open a Geek section on the wiki for > this type of links ? _____ > > From: Michael Barton [mailto:mail at michaelbarton.me.uk] To: BioRuby Mailing > List [mailto:bioruby at lists.open-bio.org] Sent: Tue, 22 Feb 2011 17:48:21 > +0100 Subject: Re: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh > C-extension > > Thank you Naohisa and Francesco for your suggestions. I will try > experimenting with these two libraries. I had also just read an interesting > article on using C extensions in Ruby which I thought might be of general > interest to the mailing list - > > http://robots.thoughtbot.com/post/1037240922 > > On Tue, Feb 22, 2011 at 06:11:20PM +0900, Naohisa GOTO wrote: > > Hi, > > > > There was SWlib, an implementation of Smith-Waterman algorithm for Ruby. > > It was written by OKUJI K. Yoshinori in 2001. Since it is very old, some > > modification would be needed for correct working. > > http://bioruby.open-bio.org/contrib/swlib/ > > > > Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > > > On Mon, 21 Feb 2011 12:06:07 -0500 Michael Barton > > wrote: > > > > > Hi, > > > > > > Does anyone know of a ruby library for doing local and global sequence > > > alignment? I'm interested in performing these kind of alignments in > > > ruby but would prefer not to call command line tools such as EMBOSS. > > > I think it could be useful to have a ruby gem which installs > > > a C-extension for allowing for reasonably fast alignment. A cursory > > > look on pubmed turned these links for C libraries. > > > > > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > > > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > > > > > Mike > > > > _______________________________________________ BioRuby Project > > - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > From chmille4 at gmail.com Tue Feb 22 15:11:48 2011 From: chmille4 at gmail.com (Chase Miller) Date: Tue, 22 Feb 2011 15:11:48 -0500 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222194309.GB5855@nku069218.hh.nku.edu> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> <20110222164821.GA2096@nku069218.hh.nku.edu> <20110222184741.GA21681@thebird.nl> <20110222194309.GB5855@nku069218.hh.nku.edu> Message-ID: My understanding is that a C extension ships the source and compiles on gem installation, whereas FFI requires multiple pre-compiled shared libraries (one for each supported platform) to ship with the gem. Maintaining all those shared libraries sounds like a lot of work. I'm not sure I understand why FFI is preferred; could someone explain it a little more in detail? Chase On Tue, Feb 22, 2011 at 2:43 PM, Michael Barton wrote: > That's useful to know. I was familiar with FFI but I didn't know it was the > preferred approach in Ruby. I'm learning C and hoping to use it where > necessary > for solving bottle necks. > > On Tue, Feb 22, 2011 at 07:47:41PM +0100, Pjotr Prins wrote: > > On Tue, Feb 22, 2011 at 11:48:21AM -0500, Michael Barton wrote: > > > Thank you Naohisa and Francesco for your suggestions. I will try > > > experimenting with these two libraries. I had also just read an > interesting > > > article on using C extensions in Ruby which I thought might be of > general > > > interest to the mailing list - > > > > > > http://robots.thoughtbot.com/post/1037240922 > > > > This discusses using a Ruby C interface. Note: it is not the easiest way. > > Especially with existing C libs you may be better off with FFI or SWIG. > The > > first makes mapping to Ruby easy, the second maps to all languages. For > most > > Ruby bindings FFI is preferred, also because it does JRuby. > > > > Binding existing libraries is usually non-trivial. Because C has no GC, > and > > buffers get passed around as function parameters. > > > > Pj. > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > From pjotr.public14 at thebird.nl Tue Feb 22 17:01:35 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 22 Feb 2011 23:01:35 +0100 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> <20110222164821.GA2096@nku069218.hh.nku.edu> <20110222184741.GA21681@thebird.nl> <20110222194309.GB5855@nku069218.hh.nku.edu> Message-ID: <20110222220135.GC22581@thebird.nl> On Tue, Feb 22, 2011 at 03:11:48PM -0500, Chase Miller wrote: > My understanding is that a C extension ships the source and compiles on gem > installation, whereas FFI requires multiple pre-compiled shared libraries > (one for each supported platform) to ship with the gem. Maintaining all > those shared libraries sounds like a lot of work. > > I'm not sure I understand why FFI is preferred; could someone explain it a > little more in detail? For the C ext you have to learn the Ruby C API. It is C. FFI allows you to define a C mapping in Ruby. You don't even have to write C code. That is the difference. The first option is what Rext does for R, and XS does for Perl. The second is more like generating C bindings, something SWIG does too. Your mileage may vary, but I am glad we can get away from that. Note that when Rext, XS or Ruby C API changes, there may be a lot of work involved (like between Perl 5 and 6). FFI mappings are more portable, also between (future) versions of Ruby, as they *generate* code. Hope that helps. But there is no reason not to dig a little. Nothing replaces experience... Pj. From Yannick.Wurm at unil.ch Wed Feb 23 01:48:21 2011 From: Yannick.Wurm at unil.ch (Yannick Wurm) Date: Wed, 23 Feb 2011 13:48:21 +0700 Subject: [BioRuby] tutorial Message-ID: <031681A4-3307-4F8D-AEF2-7B74668046E3@unil.ch> Hi all, I recently discovered pjotr's updated version of the bioruby tutorial http://thebird.nl/bioruby/Tutorial.rd.html It looks great and seems to be more recent than whats on the bioruby site. Is there any reason the old tutorial is still on the bioruby site? It's a bit confusing. Furthermore, I think newbies are more likely to follow what is on the bioruby site because: - pjotr's tutorials pagerank is lower - the "WARNING: Much of this page works, but we recommend you use the tutorial currently in the distribution as ./doc/Tutorial.rd.html. A recently updated version is here" doesn't stand out at all and so most are unlikely to see it. pjotr: maybe one thing that could make your tutorial easier to read is an index... kind regards, yannick ------------------------- Ant Genomes & Evolution http://yannick.poulet.org skype://yannickwurm From ktym at hgc.jp Wed Feb 23 02:43:47 2011 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 23 Feb 2011 16:43:47 +0900 Subject: [BioRuby] BioRuby GSoC 2011 ideas? References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> Message-ID: <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> Hi all, I just discussed with Rutger about Google Summer of Code (GSoC) 2011. If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. Attached is an announcement from NESCent, which is focused on phloinformatics. I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 http://www.open-bio.org/wiki/Google_Summer_of_Code Some ideas from our side are: for NESCent GSoC, - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) for OBF GSoC, - develop NGS-related plugins - develop a generic framework for workflow management and parallel execution of tasks - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) Regards, Toshiaki Katayama Begin forwarded message: > From: Hilmar Lapp > Date: 2011?2?22? 03:55:52JST > To: PhyloSoC Announcements > Subject: Phyloinformatics Summer of Code 2011: Call for Mentors > Reply-To: phylosoc-announce at googlegroups.com > > Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. > > Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. > > If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). > > If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. > > The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). > > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 > > We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): > > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 > > Dates: > ====== > > Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. > > Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See > http://bit.ly/soc2011-timeline for a full timeline of the whole program. > > Cheers, and we look forward to hearing from you! > > Karen Cranston > Hilmar Lapp > > (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. > > -- > You received this message because you are subscribed to the Google > Groups "Phyloinfomatics Summer of Code Announcements" group. > To unsubscribe from this group, send email to > phylosoc-announce+unsubscribe at googlegroups.com > For more options, visit this group at > http://groups.google.com/group/phylosoc-announce?hl=en From ktym at hgc.jp Wed Feb 23 04:45:36 2011 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 23 Feb 2011 18:45:36 +0900 Subject: [BioRuby] tutorial In-Reply-To: <031681A4-3307-4F8D-AEF2-7B74668046E3@unil.ch> References: <031681A4-3307-4F8D-AEF2-7B74668046E3@unil.ch> Message-ID: Hi Yannick, I agree that we should keep the latest version on the web. I'm not sure which is most recent version, http://thebird.nl/bioruby/Tutorial.rd.html https://github.com/bioruby/bioruby/blob/master/doc/Tutorial.rd but if we convert this Tutrial.rd written in RD format to rdoc format (should be easy), it will be automatically available at, http://bioruby.open-bio.org/rdoc/ however, I don't know there is a best way to synchronize it with http://bioruby.open-bio.org/wiki/Tutorial because Mediawiki format is also a different one from RD and rdoc... Any ideas? Toshiaki On 2011/02/23, at 15:48, Yannick Wurm wrote: > Hi all, > I recently discovered pjotr's updated version of the bioruby tutorial > http://thebird.nl/bioruby/Tutorial.rd.html > > It looks great and seems to be more recent than whats on the bioruby site. Is there any reason the old tutorial is still on the bioruby site? It's a bit confusing. Furthermore, I think newbies are more likely to follow what is on the bioruby site because: > - pjotr's tutorials pagerank is lower > - the "WARNING: Much of this page works, but we recommend you use the tutorial currently in the distribution as ./doc/Tutorial.rd.html. A recently updated version is here" doesn't stand out at all and so most are unlikely to see it. > > pjotr: maybe one thing that could make your tutorial easier to read is an index... > > kind regards, > > yannick > > > ------------------------- > Ant Genomes & Evolution > http://yannick.poulet.org > skype://yannickwurm > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Wed Feb 23 05:51:32 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 23 Feb 2011 11:51:32 +0100 Subject: [BioRuby] tutorial In-Reply-To: References: <031681A4-3307-4F8D-AEF2-7B74668046E3@unil.ch> Message-ID: <20110223105132.GA24543@thebird.nl> On Wed, Feb 23, 2011 at 06:45:36PM +0900, Toshiaki Katayama wrote: > however, I don't know there is a best way to synchronize it with > > http://bioruby.open-bio.org/wiki/Tutorial > > because Mediawiki format is also a different one from RD and rdoc... Any ideas? we should drop the Mediawiki version - despite the nice colours. Pj. From bonnalraoul at ingm.it Wed Feb 23 07:10:30 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 23 Feb 2011 13:10:30 +0100 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> Message-ID: <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Dear All, I remind you about the irc meeting for live discussion, I think the main topic can be GSoC 2011 I'd like to have some update about Semantic Web its reliability and if we (bioruby) are going to use it. Where? I'm available for mentoring on OBF GSoC projects. On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: > Hi all, > > I just discussed with Rutger about Google Summer of Code (GSoC) 2011. > If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. > > Attached is an announcement from NESCent, which is focused on phloinformatics. > I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). > > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 > http://www.open-bio.org/wiki/Google_Summer_of_Code > > Some ideas from our side are: > > for NESCent GSoC, > - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) > > for OBF GSoC, > - develop NGS-related plugins > - develop a generic framework for workflow management and parallel execution of tasks > - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) > > Regards, > Toshiaki Katayama > > Begin forwarded message: > >> From: Hilmar Lapp >> Date: 2011?2?22? 03:55:52JST >> To: PhyloSoC Announcements >> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors >> Reply-To: phylosoc-announce at googlegroups.com >> >> Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. >> >> Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. >> >> If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). >> >> If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. >> >> The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). >> >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >> >> We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): >> >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 >> >> Dates: >> ====== >> >> Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. >> >> Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See >> http://bit.ly/soc2011-timeline for a full timeline of the whole program. >> >> Cheers, and we look forward to hearing from you! >> >> Karen Cranston >> Hilmar Lapp >> >> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. >> >> -- >> You received this message because you are subscribed to the Google >> Groups "Phyloinfomatics Summer of Code Announcements" group. >> To unsubscribe from this group, send email to >> phylosoc-announce+unsubscribe at googlegroups.com >> For more options, visit this group at >> http://groups.google.com/group/phylosoc-announce?hl=en > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra From anurag08priyam at gmail.com Wed Feb 23 07:55:21 2011 From: anurag08priyam at gmail.com (Anurag Priyam) Date: Wed, 23 Feb 2011 18:25:21 +0530 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> Message-ID: > for OBF GSoC, > - develop NGS-related plugins > - develop a generic framework for workflow management and parallel execution of tasks > - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) Rutger had earlier informed me that he has decided to refactor my last years's GSoC work into two separate plugins - bio-nexml, and bio-rdf. While Rutger has already started to work on bio-nexml, bio-rdf still needs to take shape (which would also be a dependency for bio-nexml). Since it is very likely that the "Semantic Web Plugins" idea would relate closely to bio-rdf, I can help there. I intend to participate again in GSoC this year as a student, so I could either undertake it as a project, or, (co-)mentor *non-officially*. -- Anurag Priyam http://about.me/yeban/ From francesco.strozzi at gmail.com Wed Feb 23 08:20:35 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Wed, 23 Feb 2011 14:20:35 +0100 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Message-ID: I'm available too for mentoring or co-mentoring with Raoul, particularly on NGS plugins. In these days I'm working on the main NGS plugin and I think one interesting topic will be to develop a workflow plugin to handle multiple (and parallel) NGS tasks and also other type of bio-analyses, as discussed during the last IRC call. OBF GSoC could be a good opportunity to develop such a plugin. Cheers Francesco On Wed, Feb 23, 2011 at 13:10, Raoul Bonnal wrote: > Dear All, > I remind you about the irc meeting for live discussion, I think the main > topic can be GSoC 2011 > > I'd like to have some update about Semantic Web its reliability and if we > (bioruby) are going to use it. Where? > > I'm available for mentoring on OBF GSoC projects. > > On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: > > > Hi all, > > > > I just discussed with Rutger about Google Summer of Code (GSoC) 2011. > > If you are interested in to mentor/participate GSoC this year, please put > your ideas on this list. > > > > Attached is an announcement from NESCent, which is focused on > phloinformatics. > > I heard that Open Bio Foundation (OBF) is also considering to organize > GSoC again (not confirmed, though). > > > > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 > > http://www.open-bio.org/wiki/Google_Summer_of_Code > > > > Some ideas from our side are: > > > > for NESCent GSoC, > > - compile phyloinfo plugins for BioRuby (based on NEXML > https://github.com/rvosa/bio-nexml, forester > http://code.google.com/p/forester/ etc.) to make analysis pipeline > available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully > ;) > > > > for OBF GSoC, > > - develop NGS-related plugins > > - develop a generic framework for workflow management and parallel > execution of tasks > > - develop plugins for Semantic Web (RDF utilities, SPARQL query > interface, handling ontologies etc.) > > > > Regards, > > Toshiaki Katayama > > > > Begin forwarded message: > > > >> From: Hilmar Lapp > >> Date: 2011?2?22? 03:55:52JST > >> To: PhyloSoC Announcements > >> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors > >> Reply-To: phylosoc-announce at googlegroups.com > >> > >> Over the next 3 weeks we will be pulling together NESCent's application > to the 2011 Google Summer of Code as a mentoring organization. This is a > call for all prospective mentors, primary and secondary, to step forward. > >> > >> Participating as an organization is competitive. Over the last years the > acceptance rate for organizations has been around 30-35%. The most important > component of organization applications is the Ideas page, and specifically > the quality and suitability of the project ideas. These project ideas are > contributed by you, our mentors. In the past we have had a strong, diverse > and well-documented portfolio of ideas with different degrees of difficulty, > from different participating open-source projects, using different > programming languages. > >> > >> If you can fancy yourself serving as a mentor, or helping someone else > mentoring a student as a secondary mentor, or would like to help out in > other capacities, please contact us as soon as you can at > phylosoc-admin at nescent.org. If you have not been a mentor with us in > previous years, we'll send you guidance on what doing so involves, and how > you can contribute to our participation. We will also add everyone who is > interested in serving to our (private) mentors mailing list (at least those > who aren't already). > >> > >> If you are new to Summer of Code and wonder what it takes or what it is > like to be a mentor for us, don't hesitate to ask questions or to contact > previous mentors (see URLs below for projects that got selected). Being a > mentor does require time (see http://bit.ly/soc2011-mentortime), but our > past mentors have pretty much unanimously found it a fun and rewarding > experience. That's aside from the code a student could contribute to your > project, and, possibly most important of all in the long run, the chance to > gain a new developer. > >> > >> The initial skeleton of our 2011 Ideas page is now up here and ready for > adding project ideas and mentors(*). > >> > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 > >> > >> We will send further guidance on drafting project ideas, but for now you > can see examples of the format and scope of project ideas on the Ideas pages > from previous years (click on "Ideas"): > >> > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 > >> > >> Dates: > >> ====== > >> > >> Submission of organization applications starts Feb 28 and closes on > March 11. For project ideas to contribute to the strength of our application > they must be in reasonable shape by the morning of March 11. *If* we are > accepted, ideas can be refined (or added) between March 18-27. > >> > >> Students apply March 28-April 8, and selected students are announced > April 25. The coding period runs from May 23 to August 22. See > >> http://bit.ly/soc2011-timeline for a full timeline of the whole > program. > >> > >> Cheers, and we look forward to hearing from you! > >> > >> Karen Cranston > >> Hilmar Lapp > >> > >> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon > wiki) requires you to login. We had to disable local account creation due to > spam getting out of control. The wiki is still open, though - just login > with your OpenID. If you don't have an OpenID, the "Login with OpenID" page > has information on you can easily get one, and if you have a Google account, > you're all set to go. > >> > >> -- > >> You received this message because you are subscribed to the Google > >> Groups "Phyloinfomatics Summer of Code Announcements" group. > >> To unsubscribe from this group, send email to > >> phylosoc-announce+unsubscribe at googlegroups.com > >> For more options, visit this group at > >> http://groups.google.com/group/phylosoc-announce?hl=en > > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > -- > Ra > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From cjfields at illinois.edu Wed Feb 23 09:42:09 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 23 Feb 2011 08:42:09 -0600 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Message-ID: It's probably also a good idea to consolidate BioRuby ideas on a specific GSoC 2011 page. Not sure if Rob Buels has set that up yet, will check into it. chris On Feb 23, 2011, at 6:10 AM, Raoul Bonnal wrote: > Dear All, > I remind you about the irc meeting for live discussion, I think the main topic can be GSoC 2011 > > I'd like to have some update about Semantic Web its reliability and if we (bioruby) are going to use it. Where? > > I'm available for mentoring on OBF GSoC projects. > > On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: > >> Hi all, >> >> I just discussed with Rutger about Google Summer of Code (GSoC) 2011. >> If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. >> >> Attached is an announcement from NESCent, which is focused on phloinformatics. >> I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). >> >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >> http://www.open-bio.org/wiki/Google_Summer_of_Code >> >> Some ideas from our side are: >> >> for NESCent GSoC, >> - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) >> >> for OBF GSoC, >> - develop NGS-related plugins >> - develop a generic framework for workflow management and parallel execution of tasks >> - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) >> >> Regards, >> Toshiaki Katayama >> >> Begin forwarded message: >> >>> From: Hilmar Lapp >>> Date: 2011?2?22? 03:55:52JST >>> To: PhyloSoC Announcements >>> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors >>> Reply-To: phylosoc-announce at googlegroups.com >>> >>> Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. >>> >>> Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. >>> >>> If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). >>> >>> If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. >>> >>> The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). >>> >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>> >>> We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): >>> >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 >>> >>> Dates: >>> ====== >>> >>> Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. >>> >>> Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See >>> http://bit.ly/soc2011-timeline for a full timeline of the whole program. >>> >>> Cheers, and we look forward to hearing from you! >>> >>> Karen Cranston >>> Hilmar Lapp >>> >>> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "Phyloinfomatics Summer of Code Announcements" group. >>> To unsubscribe from this group, send email to >>> phylosoc-announce+unsubscribe at googlegroups.com >>> For more options, visit this group at >>> http://groups.google.com/group/phylosoc-announce?hl=en >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > -- > Ra > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnalraoul at ingm.it Wed Feb 23 10:11:02 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 23 Feb 2011 16:11:02 +0100 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Message-ID: Good point Chris. Do you want to join us, tomorrow ? On 23/feb/2011, at 15.42, Chris Fields wrote: > It's probably also a good idea to consolidate BioRuby ideas on a specific GSoC 2011 page. Not sure if Rob Buels has set that up yet, will check into it. > > chris > > On Feb 23, 2011, at 6:10 AM, Raoul Bonnal wrote: > >> Dear All, >> I remind you about the irc meeting for live discussion, I think the main topic can be GSoC 2011 >> >> I'd like to have some update about Semantic Web its reliability and if we (bioruby) are going to use it. Where? >> >> I'm available for mentoring on OBF GSoC projects. >> >> On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: >> >>> Hi all, >>> >>> I just discussed with Rutger about Google Summer of Code (GSoC) 2011. >>> If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. >>> >>> Attached is an announcement from NESCent, which is focused on phloinformatics. >>> I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). >>> >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>> http://www.open-bio.org/wiki/Google_Summer_of_Code >>> >>> Some ideas from our side are: >>> >>> for NESCent GSoC, >>> - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) >>> >>> for OBF GSoC, >>> - develop NGS-related plugins >>> - develop a generic framework for workflow management and parallel execution of tasks >>> - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) >>> >>> Regards, >>> Toshiaki Katayama >>> >>> Begin forwarded message: >>> >>>> From: Hilmar Lapp >>>> Date: 2011?2?22? 03:55:52JST >>>> To: PhyloSoC Announcements >>>> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors >>>> Reply-To: phylosoc-announce at googlegroups.com >>>> >>>> Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. >>>> >>>> Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. >>>> >>>> If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). >>>> >>>> If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. >>>> >>>> The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). >>>> >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>>> >>>> We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): >>>> >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 >>>> >>>> Dates: >>>> ====== >>>> >>>> Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. >>>> >>>> Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See >>>> http://bit.ly/soc2011-timeline for a full timeline of the whole program. >>>> >>>> Cheers, and we look forward to hearing from you! >>>> >>>> Karen Cranston >>>> Hilmar Lapp >>>> >>>> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "Phyloinfomatics Summer of Code Announcements" group. >>>> To unsubscribe from this group, send email to >>>> phylosoc-announce+unsubscribe at googlegroups.com >>>> For more options, visit this group at >>>> http://groups.google.com/group/phylosoc-announce?hl=en >>> >>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> -- >> Ra >> >> >> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > -- Ra From cjfields at illinois.edu Wed Feb 23 10:59:52 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 23 Feb 2011 09:59:52 -0600 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Message-ID: <7C26CA61-02C4-4424-B074-E37E6B88B565@illinois.edu> Let me know the IRC server, channel, and time, and I'll check in. Not sure how the time will sync but I can always try. chris On Feb 23, 2011, at 9:11 AM, Raoul Bonnal wrote: > Good point Chris. > Do you want to join us, tomorrow ? > On 23/feb/2011, at 15.42, Chris Fields wrote: > >> It's probably also a good idea to consolidate BioRuby ideas on a specific GSoC 2011 page. Not sure if Rob Buels has set that up yet, will check into it. >> >> chris >> >> On Feb 23, 2011, at 6:10 AM, Raoul Bonnal wrote: >> >>> Dear All, >>> I remind you about the irc meeting for live discussion, I think the main topic can be GSoC 2011 >>> >>> I'd like to have some update about Semantic Web its reliability and if we (bioruby) are going to use it. Where? >>> >>> I'm available for mentoring on OBF GSoC projects. >>> >>> On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: >>> >>>> Hi all, >>>> >>>> I just discussed with Rutger about Google Summer of Code (GSoC) 2011. >>>> If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. >>>> >>>> Attached is an announcement from NESCent, which is focused on phloinformatics. >>>> I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). >>>> >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>>> http://www.open-bio.org/wiki/Google_Summer_of_Code >>>> >>>> Some ideas from our side are: >>>> >>>> for NESCent GSoC, >>>> - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) >>>> >>>> for OBF GSoC, >>>> - develop NGS-related plugins >>>> - develop a generic framework for workflow management and parallel execution of tasks >>>> - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) >>>> >>>> Regards, >>>> Toshiaki Katayama >>>> >>>> Begin forwarded message: >>>> >>>>> From: Hilmar Lapp >>>>> Date: 2011?2?22? 03:55:52JST >>>>> To: PhyloSoC Announcements >>>>> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors >>>>> Reply-To: phylosoc-announce at googlegroups.com >>>>> >>>>> Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. >>>>> >>>>> Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. >>>>> >>>>> If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). >>>>> >>>>> If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. >>>>> >>>>> The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). >>>>> >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>>>> >>>>> We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): >>>>> >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 >>>>> >>>>> Dates: >>>>> ====== >>>>> >>>>> Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. >>>>> >>>>> Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See >>>>> http://bit.ly/soc2011-timeline for a full timeline of the whole program. >>>>> >>>>> Cheers, and we look forward to hearing from you! >>>>> >>>>> Karen Cranston >>>>> Hilmar Lapp >>>>> >>>>> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "Phyloinfomatics Summer of Code Announcements" group. >>>>> To unsubscribe from this group, send email to >>>>> phylosoc-announce+unsubscribe at googlegroups.com >>>>> For more options, visit this group at >>>>> http://groups.google.com/group/phylosoc-announce?hl=en >>>> >>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >>> -- >>> Ra >>> >>> >>> >>> >>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> > > -- > Ra > > > > From anurag08priyam at gmail.com Wed Feb 23 11:14:25 2011 From: anurag08priyam at gmail.com (Anurag Priyam) Date: Wed, 23 Feb 2011 21:44:25 +0530 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <7C26CA61-02C4-4424-B074-E37E6B88B565@illinois.edu> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> <7C26CA61-02C4-4424-B074-E37E6B88B565@illinois.edu> Message-ID: > Let me know the IRC server, channel, and time, and I'll check in. ?Not sure how the time will sync but I can always try. #bioruby on Freenode See timings at: http://bioruby.open-bio.org/wiki/BioRuby_IRC_conference -- Anurag Priyam http://about.me/yeban/ From cmzmasek at yahoo.com Thu Feb 24 14:00:08 2011 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Thu, 24 Feb 2011 11:00:08 -0800 (PST) Subject: [BioRuby] BioRuby multiple sequence alignment and phylogenetics tutorial Message-ID: <656365.18864.qm@web38406.mail.mud.yahoo.com> Hi, all: I (finally) started to work on the promised multiple sequence alignment and phylogenetics tutorial. You can see the "development" version (not much more than a scaffold at this point) here: http://code.google.com/p/forester/wiki/PhyloBioRuby (Obviously this needs to be moved once it approaches completeness.) Any comments? Please note: 1. In order to allow BioRuby to run at least a very simple phylogenetic inference 'pipeline' (unaligned sequences to phylogenetic tree), I am thinking about writing wrappers for RAxML and FastME and possibly some programs from the PHYLIP package. 2. I still need to test (and clean up) Sarah Rayburn's GSoC code ('SDI') so that it can be considered for inclusion into the main BioRuby distribution. Christian Zmasek PS. We discussed this a little on the BioRuby irc-conference 24. Feb. 2011. From bonnalraoul at ingm.it Fri Feb 25 03:52:59 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 25 Feb 2011 09:52:59 +0100 Subject: [BioRuby] BioRuby+BioGem@Ruby Social Club in Milan Message-ID: Dear All, yesterday I talked about BioRuby and BioGem projects during a Ruby Meeting in Milan. Sorry the presentation is in Italian, I'll translate it in english asap if you are interested. It was a small meeting with few people but they were very interested about our projects. I think because we are facing problems that are not so common, basically the business is more "standard" than expected :-). Many of them believe that bioinformatics is just crunching data. Others known our friends BioPerl and BioPython and nothing about BioRuby. Why ? One or two guys that know BioPython were exited about BioRuby; the answer is simple, at university they learned perl or python, ruby is just relegated to business work aka Rails. What that means for me ? Perl is an institution :-) ,Python's guys did a great job in spreading their project. How can we change the world :-) ? Talking! and in June ( I can't remember the date, around 12) there will be the Ruby Day -Italy- at University of Milano Bicocca and I'm going to help as much as possible in this event. Actually I hope to take part in the organization, everything needs to be planned, talks, tutorials.... etc I'm very surprised for a so strong and vivid interest. The meeting schedule: - Giordano Scalzo. MongoMapper , a wrapper for MongoDB - Raoul Bonnal. BioRuby and BioGem, how to create gems that can be reused from script and rails application aka engines BioGem - Andrea Reginato. Testing ed RSpec best practices. NOTE: please contribute to the document is free and open !!! -Elia Schito:TimeTap helps you track the time you spend coding on each project while in TextMate https://github.com/elia/timetap Just few link that can be of interest for Bio* projetcs, I know that Peter and Chris are reading: >>> CeBIT di Hannover nell'ambito dell'"Open >>> Source Park" >>> >>> http://www.cebit.de/exhibitor/vemar?directLink=Y854924 >>> http://www.open-source-park.com/ > www.nosqlday.it sold out (just for note) MongoUK - 21 March http://www.10gen.com/conferences/mongouk2011 Mongo France - 23 March http://lacantine.org/events/mongo-france-2011 http://www.10gen.com/conferences/mongofr2011 Mongo Berlin - 25 March http://www.10gen.com/conferences/mongoberlin2011 It would be very useful to have a shared calendar where putting this kind of events. Do we agree to use google calendar or do you have a better solution ? Ciao! -- Ra From rob.syme at gmail.com Sat Feb 26 16:36:52 2011 From: rob.syme at gmail.com (Rob Syme) Date: Sun, 27 Feb 2011 05:36:52 +0800 Subject: [BioRuby] Move your ass at this site! Message-ID: Multiple orgasms with your lover!!!.. http://ulf.lass-trocknen.de/links.php?facgoogle=366 From bonnalraoul at ingm.it Mon Feb 28 11:07:54 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Mon, 28 Feb 2011 17:07:54 +0100 Subject: [BioRuby] BestPracties for wrappers Message-ID: Dear Goto-san, if I would write a new wrapper for a new program, using Bio::Command libs, which are the best practies ? looking into the other wrappers the code is not always, let' say "standard" Could you give me some hints ? -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From cmzmasek at yahoo.com Mon Feb 28 14:14:15 2011 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Mon, 28 Feb 2011 11:14:15 -0800 (PST) Subject: [BioRuby] BestPracties for wrappers In-Reply-To: References: Message-ID: <508088.59531.qm@web38402.mail.mud.yahoo.com> Good point! I also would be interested in that! Christian ----- Original Message ---- > From: Raoul Bonnal > To: BioRuby ML > Sent: Mon, February 28, 2011 8:07:54 AM > Subject: [BioRuby] BestPracties for wrappers > > Dear Goto-san, > if I would write a new wrapper for a new program, using Bio::Command libs, >which are the best practies ? > looking into the other wrappers the code is not always, let' say "standard" > Could you give me some hints ? > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From missy at be.to Wed Feb 2 03:51:56 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Wed, 02 Feb 2011 12:51:56 +0900 Subject: [BioRuby] Rakefiles for the Dindel workflow Message-ID: <4D48D4DC.3020808@be.to> Hi all, I wrote a rakefile for the Dindel workflow. Dindel is a toolkit to call small indels from mapped short-read data (BAM files). See http://www.sanger.ac.uk/resources/software/dindel/ . The rakefile is available at https://github.com/misshie/RakefileDindel . I think my rakefile is a good example of "dynamic task definition". During Stage 3 of the workflow, Dindel generates over 300 files for exome data. Although the file naming rule is known before running rake, the number of files to be generated is unknown at the time. van der Aalst et al. (2003) have shown this pattern as "pattern 14: multiple instances with a priori runtime knowledge". Rakefiles can describe this pattern using Rake::Task#invoke. Furthermore, this rakefile demonstrates effectiveness of Pwrake. Stage 3 is a typical embarrassingly parallel problem. To improve rakefile readability, I separated a Rakefile into Rakefile, Rakefile.invoke, and Rakefile.helper. Rakefile is workflow description. Rakefile.invoke is command-lines to invoke tools. Rakefile.helper has helper methods making Rakefile simpler. Previously Yannick Wurm has shown a rakefile "cdsToAlignmentToTree" at https://github.com/yannickwurm/tidbits/ . The rakefile handles exceptions carefully. Mine does not. Yannick's approach is important because sometimes error messages in rakefiles are not intuitive. So far, my workflow does not use BioRuby at all. Raoul Bonnal have suggested BioRuby-rake integration replying Yannick's post. Introducing modular task definition to rake is what we need but not very easy because each workflow step in a rakefiles is linked too tight. Introducing a BioRuby plug-in to support common helper methods simplifying rakefiles seems easier. It may contain my Rakefile.helper, and Yannick's helper methods and exception handling. I will try to write a small plug-in for a while. Sincerely yours, Hiro. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From bonnalraoul at ingm.it Wed Feb 2 09:41:47 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 2 Feb 2011 10:41:47 +0100 Subject: [BioRuby] Rakefiles for the Dindel workflow In-Reply-To: <4D48D4DC.3020808@be.to> References: <4D48D4DC.3020808@be.to> Message-ID: <5881720A-141D-41A5-A872-0FB004DA9C5D@ingm.it> Hi Hiro, seems an interesting approach, we could discuss this e-mail tomorrow during the irc meeting. is it fine for you ? I can't catch how do you use pwrake, sorry probably I missed something, I mean the benefit. On 02/feb/2011, at 04.51, MISHIMA, Hiroyuki wrote: > Hi all, > > I wrote a rakefile for the Dindel workflow. Dindel is a toolkit to call > small indels from mapped short-read data (BAM files). See > http://www.sanger.ac.uk/resources/software/dindel/ . > > The rakefile is available at https://github.com/misshie/RakefileDindel . > > I think my rakefile is a good example of "dynamic task definition". > During Stage 3 of the workflow, Dindel generates over 300 files for > exome data. Although the file naming rule is known before running rake, > the number of files to be generated is unknown at the time. > > van der Aalst et al. (2003) have shown this pattern as "pattern 14: > multiple instances with a priori runtime knowledge". Rakefiles can > describe this pattern using Rake::Task#invoke. > > Furthermore, this rakefile demonstrates effectiveness of Pwrake. Stage 3 > is a typical embarrassingly parallel problem. > > To improve rakefile readability, I separated a Rakefile into Rakefile, > Rakefile.invoke, and Rakefile.helper. Rakefile is workflow description. > Rakefile.invoke is command-lines to invoke tools. Rakefile.helper has > helper methods making Rakefile simpler. > > Previously Yannick Wurm has shown a rakefile "cdsToAlignmentToTree" at > https://github.com/yannickwurm/tidbits/ . The rakefile handles > exceptions carefully. Mine does not. Yannick's approach is important > because sometimes error messages in rakefiles are not intuitive. > > So far, my workflow does not use BioRuby at all. Raoul Bonnal have > suggested BioRuby-rake integration replying Yannick's post. Introducing > modular task definition to rake is what we need but not very easy > because each workflow step in a rakefiles is linked too tight. > > Introducing a BioRuby plug-in to support common helper methods > simplifying rakefiles seems easier. It may contain my Rakefile.helper, > and Yannick's helper methods and exception handling. > > I will try to write a small plug-in for a while. > > Sincerely yours, > Hiro. > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- R.J.P.B. From bonnalraoul at ingm.it Wed Feb 2 09:42:37 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 2 Feb 2011 10:42:37 +0100 Subject: [BioRuby] SRA and NCBI Message-ID: <02654276-648A-47CF-B24E-B05E50FB8428@ingm.it> Take a look for downloading data from ncbi http://www.ncbi.nlm.nih.gov/books/NBK47540/ Do we want to support sra or just the tool kit ? -- R.J.P.B. From missy at be.to Wed Feb 2 13:48:36 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Wed, 02 Feb 2011 22:48:36 +0900 Subject: [BioRuby] Rakefiles for the Dindel workflow In-Reply-To: <5881720A-141D-41A5-A872-0FB004DA9C5D@ingm.it> References: <4D48D4DC.3020808@be.to> <5881720A-141D-41A5-A872-0FB004DA9C5D@ingm.it> Message-ID: <4D4960B4.3090003@be.to> Hi, I will attend tomorrow's irc meeting. See you all at #bioruby. And, the benefit to use Pwrake is the followings: Rakefiles for Rake and Pwrake is fully compatible. However, Pwrake automatically finds "embarrassingly parallel" steps and smartly distributes processes via ssh. For example, when nodefile is "localhost 16", Pwrake tries to keep running 16 processes simultaneously. The function is indispensable to run more than 300 processes in Dindel's stage 3. Sincerely yours, Hiro Raoul Bonnal wrote (2011/02/02 18:41): > Hi Hiro, seems an interesting approach, we could discuss this e-mail > tomorrow during the irc meeting. is it fine for you ? > > I can't catch how do you use pwrake, sorry probably I missed > something, I mean the benefit. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From mictadlo at gmail.com Thu Feb 3 08:16:25 2011 From: mictadlo at gmail.com (Michal) Date: Thu, 03 Feb 2011 18:16:25 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: References: <4D454E91.1080604@gmail.com> Message-ID: <4D4A6459.5050205@gmail.com> Dear Raoul, I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: $ tar xvfz ruby-1.9.2-p136.tar.gz $ cd ruby-1.9.2-p136/ $ ./configure --prefix=/home/mictadlo/apps/ruby $ make $ make install $ vim ~/.bashrc export APPS=/home/mictadlo/apps export RUBY_HOME=$APPS/ruby export LD_LIBRARY_PATH=/RUBY_HOME/lib PATH=$RUBY_HOME/bin:$PATH $ . ~/.bashrc $ ruby -v ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] $ gem install ffi Building native extensions. This could take a while... Successfully installed ffi-1.0.5 1 gem installed Installing ri documentation for ffi-1.0.5... Installing RDoc documentation for ffi-1.0.5... ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ remote: Counting objects: 92, done. remote: Compressing objects: 100% (84/84), done. remote: Total 92 (delta 21), reused 0 (delta 0) Unpacking objects: 100% (92/92), done. ~/Downloads/git/bioruby-samtools$ rake test (in /home/mictadlo/Downloads/git/bioruby-samtools) rake aborted! no such file to load -- bundler :29:in `require' :29:in `require' /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' /home/mictadlo/apps/ruby/bin/rake:31:in `
' What did I wrong? Thank you in advance. Michal On 01/31/2011 08:11 PM, Raoul Bonnal wrote: > Dear Michal, > please check this out: > > https://github.com/helios/bioruby-samtools > > This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. > I need to test the linux library because I'm developing under osx. > If the libbam.a is wrong please give me the right one and I'll add it to the repo. > Also note that the library has been compiled for 64bit. > > Ciao! > > On 30/gen/2011, at 12.42, Michal wrote: > >> Hi, >> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >> >> What did I wrong? >> >> Michal >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > -- > R.J.P.B. > > > > > From mictadlo at gmail.com Thu Feb 3 09:55:07 2011 From: mictadlo at gmail.com (Michal) Date: Thu, 03 Feb 2011 19:55:07 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> Message-ID: <4D4A7B7B.2000103@gmail.com> Hi Philipp, Bundler fix one problem, but I have got a new one: $ gem install bundler Successfully installed bundler-1.0.10 1 gem installed Installing ri documentation for bundler-1.0.10... Installing RDoc documentation for bundler-1.0.10... ~/Downloads/git/bioruby-samtools$ rake test (in /home/uqmlore1/Downloads/git/bioruby-samtools) Could not find bio-1.4.1 in any of the sources Run `bundle install` to install missing gems $ irb irb(main):001:0> require "bio" => true irb(main):002:0> exit $ bioruby Loading config (/home/uqmlore1/.bioruby/shell/session/config) ... done Loading object (/home/uqmlore1/.bioruby/shell/session/object) ... Error: Failed to load (/home/uqmlore1/.bioruby/shell/session/object) : marshal data too short done . . . B i o R u b y i n t h e s h e l l . . . Version : BioRuby 1.4.1 / Ruby 1.9.2 Thank you in advance. Michal On 02/03/2011 07:03 PM, Philipp Comans wrote: > Try gem install bundler > > Am 03.02.2011 um 09:16 schrieb Michal: > >> Dear Raoul, >> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: >> $ tar xvfz ruby-1.9.2-p136.tar.gz >> $ cd ruby-1.9.2-p136/ >> $ ./configure --prefix=/home/mictadlo/apps/ruby >> $ make >> $ make install >> $ vim ~/.bashrc >> export APPS=/home/mictadlo/apps >> export RUBY_HOME=$APPS/ruby >> export LD_LIBRARY_PATH=/RUBY_HOME/lib >> PATH=$RUBY_HOME/bin:$PATH >> $ . ~/.bashrc >> $ ruby -v >> ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] >> >> $ gem install ffi >> Building native extensions. This could take a while... >> Successfully installed ffi-1.0.5 >> 1 gem installed >> Installing ri documentation for ffi-1.0.5... >> Installing RDoc documentation for ffi-1.0.5... >> >> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git >> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ >> remote: Counting objects: 92, done. >> remote: Compressing objects: 100% (84/84), done. >> remote: Total 92 (delta 21), reused 0 (delta 0) >> Unpacking objects: 100% (92/92), done. >> >> ~/Downloads/git/bioruby-samtools$ rake test >> (in /home/mictadlo/Downloads/git/bioruby-samtools) >> rake aborted! >> no such file to load -- bundler >> :29:in `require' >> :29:in `require' >> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' >> /home/mictadlo/apps/ruby/bin/rake:31:in `
' >> >> What did I wrong? >> >> Thank you in advance. >> >> Michal >> >> On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >>> Dear Michal, >>> please check this out: >>> >>> https://github.com/helios/bioruby-samtools >>> >>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. >>> I need to test the linux library because I'm developing under osx. >>> If the libbam.a is wrong please give me the right one and I'll add it to the repo. >>> Also note that the library has been compiled for 64bit. >>> >>> Ciao! >>> >>> On 30/gen/2011, at 12.42, Michal wrote: >>> >>>> Hi, >>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >>>> >>>> What did I wrong? >>>> >>>> Michal >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> -- >>> R.J.P.B. >>> >>> >>> >>> >>> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby From tomoakin at kenroku.kanazawa-u.ac.jp Thu Feb 3 10:10:28 2011 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Thu, 3 Feb 2011 19:10:28 +0900 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4A6459.5050205@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> Message-ID: <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> Hi, As it says. > Run `bundle install` to install missing gems $ bundle install will install all other required gems. The next thing to do is for the error: /home/tomoaki/ruby192p136/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/ library.rb:75:in `block in ffi_lib': Could not open library '/home/ tomoaki/bioruby-samtools/lib/bio/db/sam/external/libbam.a': Its natural that a dynamic library should be made for the purpose as is in Mac OS X. $ make dylib in the latest samtools and copy libbam.so.1 to bioruby-samtools/lib/ bio/db/sam/external/ ------------CUT diff --git a/lib/bio/db/sam/external/libbam.a b/lib/bio/db/sam/ external/libbam.a index 0f231ef..aa1b225 100644 Binary files a/lib/bio/db/sam/external/libbam.a and b/lib/bio/db/sam/ external/libbam.a differ diff --git a/lib/bio/db/sam/library.rb b/lib/bio/db/sam/library.rb index bb78515..e9f8b6e 100644 --- a/lib/bio/db/sam/library.rb +++ b/lib/bio/db/sam/library.rb @@ -9,7 +9,7 @@ module Bio #TODO refactor this piece of code in all the files lib_os = case RUBY_PLATFORM when /linux/ - 'a' + 'so.1' when /darwin/ 'dylib' when /windows/ @@ -22,4 +22,4 @@ module Bio end #Library end #Sam end #DB -end #Bio \ No newline at end of file +end #Bio ------------CUT Then finally reached this state $ ~/ruby192p136/bin/rake (in /home/tomoaki/bioruby-samtools) /home/tomoaki/ruby192p136/bin/ruby -I"lib:lib:test" "/home/tomoaki/ ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio- samtools.rb" Loaded suite /home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/ rake_test_loader Started F Finished in 0.000321 seconds. 1) Failure: test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: hey buddy, you should probably rename this file and start testing for real Loading seems ok. I'm not sure if this is bad or ok. Best regards -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan On 2011/02/03, at 17:16, Michal wrote: > Dear Raoul, > I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 > 64bit in the following way: > $ tar xvfz ruby-1.9.2-p136.tar.gz > $ cd ruby-1.9.2-p136/ > $ ./configure --prefix=/home/mictadlo/apps/ruby > $ make > $ make install > $ vim ~/.bashrc > export APPS=/home/mictadlo/apps > export RUBY_HOME=$APPS/ruby > export LD_LIBRARY_PATH=/RUBY_HOME/lib > PATH=$RUBY_HOME/bin:$PATH > $ . ~/.bashrc > $ ruby -v > ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] > > $ gem install ffi > Building native extensions. This could take a while... > Successfully installed ffi-1.0.5 > 1 gem installed > Installing ri documentation for ffi-1.0.5... > Installing RDoc documentation for ffi-1.0.5... > > ~/Downloads/git$ git clone https://github.com/helios/bioruby- > samtools.git > Initialized empty Git repository in /home/mictadlo/Downloads/git/ > bioruby-samtools/.git/ > remote: Counting objects: 92, done. > remote: Compressing objects: 100% (84/84), done. > remote: Total 92 (delta 21), reused 0 (delta 0) > Unpacking objects: 100% (92/92), done. > > ~/Downloads/git/bioruby-samtools$ rake test > (in /home/mictadlo/Downloads/git/bioruby-samtools) > rake aborted! > no such file to load -- bundler > :29:in `require' > :29:in `require' > /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in ` (required)>' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in > `raw_load_rakefile' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in > load_rakefile' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in > `standard_exception_handling' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in > `load_rakefile' > /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' > /home/mictadlo/apps/ruby/bin/rake:31:in `
' > > What did I wrong? > > Thank you in advance. > > Michal > > On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >> Dear Michal, >> please check this out: >> >> https://github.com/helios/bioruby-samtools >> >> This is the inital port of samtools-ruby as plugin. It comes with >> library for osx and linux, no windows. >> I need to test the linux library because I'm developing under osx. >> If the libbam.a is wrong please give me the right one and I'll add >> it to the repo. >> Also note that the library has been compiled for 64bit. >> >> Ciao! >> >> On 30/gen/2011, at 12.42, Michal wrote: >> >>> Hi, >>> I have tried to install samtools-ruby on ruby 1.9.2, but I have >>> failed. I have already posted this problem on https://github.com/ >>> homonecloco/samtools-ruby/issues#issue/3 , but I have not got any >>> response. >>> >>> What did I wrong? >>> >>> Michal >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> -- >> R.J.P.B. >> >> >> >> >> > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From mictadlo at gmail.com Thu Feb 3 11:23:40 2011 From: mictadlo at gmail.com (Michal) Date: Thu, 03 Feb 2011 21:23:40 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: <1BC9C29B-EE9E-4F9A-B96B-27FD341204E1@googlemail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <4D4A7B7B.2000103@gmail.com> <1BC9C29B-EE9E-4F9A-B96B-27FD341204E1@googlemail.com> Message-ID: <4D4A903C.2030807@gmail.com> Hi Philipp, Bundle solved this problem, but after rake install I can not call rake test. $ bundle install Fetching source index for http://rubygems.org/ Using rake (0.8.7) Installing bio (1.4.1) Using bundler (1.0.10) Using ffi (1.0.5) Installing git (1.2.5) Installing jeweler (1.5.2) Installing rcov (0.9.9) with native extensions Installing shoulda (2.11.3) Your bundle is complete! Use `bundle show [gemname]` to see where a bundled gem is installed. $ rake install (in /home/mictadlo/Downloads/git/bioruby-samtools) WARNING: no rubyforge_project specified Successfully built RubyGem Name: bio-samtools Version: 0.0.0 File: bio-samtools-0.0.0.gem Executing "ruby -S gem install ./pkg/bio-samtools-0.0.0.gem": ruby -S gem install ./pkg/bio-samtools-0.0.0.gem Successfully installed bio-samtools-0.0.0 1 gem installed Installing ri documentation for bio-samtools-0.0.0... Installing RDoc documentation for bio-samtools-0.0.0... $ rake test (in /home/mictadlo/Downloads/git/bioruby-samtools) /home/mictadlo/apps/ruby/bin/ruby -I"lib:lib:test" "/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in `block in ffi_lib': Could not open library '/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.a': /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.a: invalid ELF header (LoadError) from /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in `map' from /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in `ffi_lib' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:12:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:8:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:7:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:6:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:5:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `' from test/test_bio-samtools.rb:1:in `require' from test/test_bio-samtools.rb:1:in `' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `load' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `block in
' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `each' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `
' rake aborted! Command failed with status (1): [/home/mictadlo/apps/ruby/bin/ruby -I"lib:l...] /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:993:in `block in sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1027:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:115:in `block (2 levels) in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1110:in `verbose' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:100:in `block in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `block in execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:595:in `block in invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/monitor.rb:201:in `mon_synchronize' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:588:in `invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:581:in `invoke' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2041:in `invoke_task' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block (2 levels) in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2013:in `top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1992:in `run' /home/mictadlo/apps/ruby/bin/rake:31:in `
' What did I wrong? Michal On 02/03/2011 08:06 PM, Philipp Comans wrote: > Hi Michal, > have you tried running > > bundle install > rake install > > In order to install the missing gems? > I see that you have bio installed but maybe it's missing something else. > > The error about "marshal data too short" went through the mailing list a few days ago, I think it is currently being worked on. > > Hope that helps! > > Best, > > Philipp > > Am 03.02.2011 um 10:55 schrieb Michal: > >> Hi Philipp, >> Bundler fix one problem, but I have got a new one: >> >> $ gem install bundler >> Successfully installed bundler-1.0.10 >> 1 gem installed >> Installing ri documentation for bundler-1.0.10... >> Installing RDoc documentation for bundler-1.0.10... >> >> ~/Downloads/git/bioruby-samtools$ rake test >> (in /home/uqmlore1/Downloads/git/bioruby-samtools) >> Could not find bio-1.4.1 in any of the sources >> Run `bundle install` to install missing gems >> >> $ irb >> irb(main):001:0> require "bio" >> => true >> irb(main):002:0> exit >> >> $ bioruby >> Loading config (/home/uqmlore1/.bioruby/shell/session/config) ... done >> Loading object (/home/uqmlore1/.bioruby/shell/session/object) ... Error: Failed to load (/home/uqmlore1/.bioruby/shell/session/object) : marshal data too short >> done >> >> . . . B i o R u b y i n t h e s h e l l . . . >> >> Version : BioRuby 1.4.1 / Ruby 1.9.2 >> >> >> Thank you in advance. >> >> Michal >> >> >> On 02/03/2011 07:03 PM, Philipp Comans wrote: >>> Try gem install bundler >>> >>> Am 03.02.2011 um 09:16 schrieb Michal: >>> >>>> Dear Raoul, >>>> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: >>>> $ tar xvfz ruby-1.9.2-p136.tar.gz >>>> $ cd ruby-1.9.2-p136/ >>>> $ ./configure --prefix=/home/mictadlo/apps/ruby >>>> $ make >>>> $ make install >>>> $ vim ~/.bashrc >>>> export APPS=/home/mictadlo/apps >>>> export RUBY_HOME=$APPS/ruby >>>> export LD_LIBRARY_PATH=/RUBY_HOME/lib >>>> PATH=$RUBY_HOME/bin:$PATH >>>> $ . ~/.bashrc >>>> $ ruby -v >>>> ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] >>>> >>>> $ gem install ffi >>>> Building native extensions. This could take a while... >>>> Successfully installed ffi-1.0.5 >>>> 1 gem installed >>>> Installing ri documentation for ffi-1.0.5... >>>> Installing RDoc documentation for ffi-1.0.5... >>>> >>>> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git >>>> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ >>>> remote: Counting objects: 92, done. >>>> remote: Compressing objects: 100% (84/84), done. >>>> remote: Total 92 (delta 21), reused 0 (delta 0) >>>> Unpacking objects: 100% (92/92), done. >>>> >>>> ~/Downloads/git/bioruby-samtools$ rake test >>>> (in /home/mictadlo/Downloads/git/bioruby-samtools) >>>> rake aborted! >>>> no such file to load -- bundler >>>> :29:in `require' >>>> :29:in `require' >>>> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' >>>> /home/mictadlo/apps/ruby/bin/rake:31:in `
' >>>> >>>> What did I wrong? >>>> >>>> Thank you in advance. >>>> >>>> Michal >>>> >>>> On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >>>>> Dear Michal, >>>>> please check this out: >>>>> >>>>> https://github.com/helios/bioruby-samtools >>>>> >>>>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. >>>>> I need to test the linux library because I'm developing under osx. >>>>> If the libbam.a is wrong please give me the right one and I'll add it to the repo. >>>>> Also note that the library has been compiled for 64bit. >>>>> >>>>> Ciao! >>>>> >>>>> On 30/gen/2011, at 12.42, Michal wrote: >>>>> >>>>>> Hi, >>>>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >>>>>> >>>>>> What did I wrong? >>>>>> >>>>>> Michal >>>>>> _______________________________________________ >>>>>> BioRuby Project - http://www.bioruby.org/ >>>>>> BioRuby mailing list >>>>>> BioRuby at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>>> -- >>>>> R.J.P.B. >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnalraoul at ingm.it Thu Feb 3 11:56:00 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Thu, 3 Feb 2011 12:56:00 +0100 Subject: [BioRuby] samtools-ruby In-Reply-To: <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> Message-ID: <970B13D0-ADD4-478E-ABDB-6DBB7CD16DC7@ingm.it> Thanks Tomoaki I missed the linux lib sorry, could you send me that library I'll add it to the repo. so.1 fixed On 03/feb/2011, at 11.10, Tomoaki NISHIYAMA wrote: > Hi, > > As it says. > >> Run `bundle install` to install missing gems > > > $ bundle install > > will install all other required gems. > > The next thing to do is for the error: > > /home/tomoaki/ruby192p136/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in `block in ffi_lib': Could not open library '/home/tomoaki/bioruby-samtools/lib/bio/db/sam/external/libbam.a': > > Its natural that a dynamic library should be made for the purpose as is in Mac OS X. > > $ make dylib > in the latest samtools and copy libbam.so.1 to bioruby-samtools/lib/bio/db/sam/external/ > > > ------------CUT > diff --git a/lib/bio/db/sam/external/libbam.a b/lib/bio/db/sam/external/libbam.a > index 0f231ef..aa1b225 100644 > Binary files a/lib/bio/db/sam/external/libbam.a and b/lib/bio/db/sam/external/libbam.a differ > diff --git a/lib/bio/db/sam/library.rb b/lib/bio/db/sam/library.rb > index bb78515..e9f8b6e 100644 > --- a/lib/bio/db/sam/library.rb > +++ b/lib/bio/db/sam/library.rb > @@ -9,7 +9,7 @@ module Bio > #TODO refactor this piece of code in all the files > lib_os = case RUBY_PLATFORM > when /linux/ > - 'a' > + 'so.1' > when /darwin/ > 'dylib' > when /windows/ > @@ -22,4 +22,4 @@ module Bio > end #Library > end #Sam > end #DB > -end #Bio > \ No newline at end of file > +end #Bio > ------------CUT > > Then finally reached this state > > $ ~/ruby192p136/bin/rake > (in /home/tomoaki/bioruby-samtools) > /home/tomoaki/ruby192p136/bin/ruby -I"lib:lib:test" "/home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" > Loaded suite /home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader > Started > F > Finished in 0.000321 seconds. > > 1) Failure: > test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: > hey buddy, you should probably rename this file and start testing for real > > Loading seems ok. > I'm not sure if this is bad or ok. > > Best regards > -- > Tomoaki NISHIYAMA > > Advanced Science Research Center, > Kanazawa University, > 13-1 Takara-machi, > Kanazawa, 920-0934, Japan > > > On 2011/02/03, at 17:16, Michal wrote: > >> Dear Raoul, >> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: >> $ tar xvfz ruby-1.9.2-p136.tar.gz >> $ cd ruby-1.9.2-p136/ >> $ ./configure --prefix=/home/mictadlo/apps/ruby >> $ make >> $ make install >> $ vim ~/.bashrc >> export APPS=/home/mictadlo/apps >> export RUBY_HOME=$APPS/ruby >> export LD_LIBRARY_PATH=/RUBY_HOME/lib >> PATH=$RUBY_HOME/bin:$PATH >> $ . ~/.bashrc >> $ ruby -v >> ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] >> >> $ gem install ffi >> Building native extensions. This could take a while... >> Successfully installed ffi-1.0.5 >> 1 gem installed >> Installing ri documentation for ffi-1.0.5... >> Installing RDoc documentation for ffi-1.0.5... >> >> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git >> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ >> remote: Counting objects: 92, done. >> remote: Compressing objects: 100% (84/84), done. >> remote: Total 92 (delta 21), reused 0 (delta 0) >> Unpacking objects: 100% (92/92), done. >> >> ~/Downloads/git/bioruby-samtools$ rake test >> (in /home/mictadlo/Downloads/git/bioruby-samtools) >> rake aborted! >> no such file to load -- bundler >> :29:in `require' >> :29:in `require' >> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' >> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' >> /home/mictadlo/apps/ruby/bin/rake:31:in `
' >> >> What did I wrong? >> >> Thank you in advance. >> >> Michal >> >> On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >>> Dear Michal, >>> please check this out: >>> >>> https://github.com/helios/bioruby-samtools >>> >>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. >>> I need to test the linux library because I'm developing under osx. >>> If the libbam.a is wrong please give me the right one and I'll add it to the repo. >>> Also note that the library has been compiled for 64bit. >>> >>> Ciao! >>> >>> On 30/gen/2011, at 12.42, Michal wrote: >>> >>>> Hi, >>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >>>> >>>> What did I wrong? >>>> >>>> Michal >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> -- >>> R.J.P.B. >>> >>> >>> >>> >>> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > -- R.J.P.B. From missy at be.to Fri Feb 4 05:22:42 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Fri, 04 Feb 2011 14:22:42 +0900 Subject: [BioRuby] Rakefile for the GATK workflow Message-ID: <4D4B8D22.10502@be.to> Hi all, I did my assignment at last IRC meeting. 1) I updated the Workflows page in the BioRuby wiki. see http://bioruby.open-bio.org/wiki/Workflows I added Michael Barton's comment about Boson, and pointers to lists of job schedulers. 2) I uploaded another rakefile sample for the GATK workflow. see https://github.com/misshie/RakefileGATK Broad institutes's Genome Analysis Toolkit (GATK) is a toolkit to detect genomic variation (mainly SNVs) from mapped NGS short reads data (BAM files). It is consists of many Java programs and requires long command-line options. Moreover, GATK team changes their recommended workflow frequently because of active development. Thus well-organized workflow management is preferable. My rakefiles are still not well-organized. Not DRY. Please let me know your comment. Sincerely yours, Hiro. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From mictadlo at gmail.com Fri Feb 4 08:01:25 2011 From: mictadlo at gmail.com (Michal) Date: Fri, 04 Feb 2011 18:01:25 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> Message-ID: <4D4BB255.7030703@gmail.com> Hello, Still problems after the following steps: ~/Downloads/samtools-0.1.12a $ make dylib ~/Downloads/samtools-0.1.12a $ cp libbam.so.1 ../git/bioruby-samtools/lib/bio/db/sam/external/ ~/Downloads/samtools-0.1.12a $ ls ../git/bioruby-samtools/lib/bio/db/sam/external/ libbam.a libbam.dylib libbam.so.1 ~/Downloads/samtools-0.1.12a $ cat ../git/bioruby-samtools/lib/bio/db/sam/library.rb module Bio module DB module SAM module Library #IMPORTANT NOTE: Windows library is missing in this distribution # Return the path with the file name of the library for the specific operating system def filename #TODO refactor this piece of code in all the files lib_os = case RUBY_PLATFORM when /linux/ 'so.1' when /darwin/ 'dylib' when /windows/ 'dll' end File.join(File.expand_path(File.dirname(__FILE__)),'external',"libbam.#{lib_os}") end #filename module_function :filename end #Library end #Sam end #DB end #Bio ~/Downloads/git/bioruby-samtools$ rake test (in /home/mictadlo/Downloads/git/bioruby-samtools) /home/mictadlo/apps/ruby/bin/ruby -I"lib:lib:test" "/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in `block in ffi_lib': Could not open library '/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.so.1': /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.so.1: undefined symbol: bam_nt16_nt4_table (LoadError) from /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in `map' from /home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in `ffi_lib' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:12:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:8:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:7:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:6:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:5:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in `' from /home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `require' from /home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `' from test/test_bio-samtools.rb:1:in `require' from test/test_bio-samtools.rb:1:in `' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `load' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `block in
' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `each' from /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `
' rake aborted! Command failed with status (1): [/home/mictadlo/apps/ruby/bin/ruby -I"lib:l...] /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:993:in `block in sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1027:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:115:in `block (2 levels) in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1110:in `verbose' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:100:in `block in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `block in execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:595:in `block in invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/monitor.rb:201:in `mon_synchronize' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:588:in `invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:581:in `invoke' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2041:in `invoke_task' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block (2 levels) in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2013:in `top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1992:in `run' /home/mictadlo/apps/ruby/bin/rake:31:in `
' ~/Downloads/git/bioruby-samtools$ ls /home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/ libbam.a libbam.dylib libbam.so.1 What did I forget to do? Thank you in advance. Michal On 02/03/2011 08:10 PM, Tomoaki NISHIYAMA wrote: > Hi, > > As it says. > >> Run `bundle install` to install missing gems > > > $ bundle install > > will install all other required gems. > > The next thing to do is for the error: > > /home/tomoaki/ruby192p136/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in > `block in ffi_lib': Could not open library > '/home/tomoaki/bioruby-samtools/lib/bio/db/sam/external/libbam.a': > > Its natural that a dynamic library should be made for the purpose as > is in Mac OS X. > > $ make dylib > in the latest samtools and copy libbam.so.1 to > bioruby-samtools/lib/bio/db/sam/external/ > > > ------------CUT > diff --git a/lib/bio/db/sam/external/libbam.a > b/lib/bio/db/sam/external/libbam.a > index 0f231ef..aa1b225 100644 > Binary files a/lib/bio/db/sam/external/libbam.a and > b/lib/bio/db/sam/external/libbam.a differ > diff --git a/lib/bio/db/sam/library.rb b/lib/bio/db/sam/library.rb > index bb78515..e9f8b6e 100644 > --- a/lib/bio/db/sam/library.rb > +++ b/lib/bio/db/sam/library.rb > @@ -9,7 +9,7 @@ module Bio > #TODO refactor this piece of code in all the files > lib_os = case RUBY_PLATFORM > when /linux/ > - 'a' > + 'so.1' > when /darwin/ > 'dylib' > when /windows/ > @@ -22,4 +22,4 @@ module Bio > end #Library > end #Sam > end #DB > -end #Bio > \ No newline at end of file > +end #Bio > ------------CUT > > Then finally reached this state > > $ ~/ruby192p136/bin/rake > (in /home/tomoaki/bioruby-samtools) > /home/tomoaki/ruby192p136/bin/ruby -I"lib:lib:test" > "/home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader.rb" > "test/test_bio-samtools.rb" > Loaded suite > /home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader > Started > F > Finished in 0.000321 seconds. > > 1) Failure: > test: BioSamtools should probably rename this file and start testing > for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: > hey buddy, you should probably rename this file and start testing for > real > > Loading seems ok. > I'm not sure if this is bad or ok. > > Best regards From tomoakin at kenroku.kanazawa-u.ac.jp Fri Feb 4 08:31:22 2011 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Fri, 4 Feb 2011 17:31:22 +0900 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4BB255.7030703@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> Message-ID: Hi, > ~/Downloads/samtools-0.1.12a The *latest* samtools which I used was r910 via svn yesterday. r854 produced the same error as you have shown. Samtools is under very active development, as seen from the mailing list flow. So, some change in the samtools code made this difference, and its a bit difficult to keep track with all the update. -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan From bonnalraoul at ingm.it Fri Feb 4 10:33:05 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 4 Feb 2011 11:33:05 +0100 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4BB116.4010300@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <970B13D0-ADD4-478E-ABDB-6DBB7CD16DC7@ingm.it> <4D4BB116.4010300@gmail.com> Message-ID: <49287604-38A3-4058-A765-4B73F1B46A38@ingm.it> Thanks, please not that I found a problem using TopHat with samtools 0.1.12a I sent a mail to TopHat's developer but I didn't receive any answer yet. this is the original message : I'm Raoul a bioinformaticians, I'll start working on illumina data set in few days; in the mean time my group is doing tests. So, I have installed all the software, latest releases and today running my first alignment with tophat I got this error: [Fri Jan 28 10:43:20 2011] Checking for Samtools Traceback (most recent call last): File "/usr/local/bin/tophat", line 2223, in ? sys.exit(main()) File "/usr/local/bin/tophat", line 2136, in main check_samtools() File "/usr/local/bin/tophat", line 877, in check_samtools samtools_version = get_samtools_version() File "/usr/local/bin/tophat", line 864, in get_samtools_version samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')] ValueError: invalid literal for int(): 12a My samtools is Program: samtools (Tools for alignments in the SAM format) Version: 0.1.12a (r862) so i fixed the line #864 with import re samtools_version = [int(re.sub('[a-z]','',x.split('-')[0])) for x in version_val.split('.')] I know that it's quite ugly solution but .... I'm a ruby man :-) and I want to let you know that we, bioruby dev team, are putting a lot of effort to support your suite. Cheers. On 04/feb/2011, at 08.56, Michal wrote: > Please find attached the libbam.so.1 of samtools-0.1.12a. > > > On 02/03/2011 09:56 PM, Raoul Bonnal wrote: >> Thanks Tomoaki >> I missed the linux lib sorry, could you send me that library I'll add it to the repo. >> so.1 fixed >> >> On 03/feb/2011, at 11.10, Tomoaki NISHIYAMA wrote: >> >>> Hi, >>> >>> As it says. >>> >>>> Run `bundle install` to install missing gems >>> >>> $ bundle install >>> >>> will install all other required gems. >>> >>> The next thing to do is for the error: >>> >>> /home/tomoaki/ruby192p136/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in `block in ffi_lib': Could not open library '/home/tomoaki/bioruby-samtools/lib/bio/db/sam/external/libbam.a': >>> >>> Its natural that a dynamic library should be made for the purpose as is in Mac OS X. >>> >>> $ make dylib >>> in the latest samtools and copy libbam.so.1 to bioruby-samtools/lib/bio/db/sam/external/ >>> >>> >>> ------------CUT >>> diff --git a/lib/bio/db/sam/external/libbam.a b/lib/bio/db/sam/external/libbam.a >>> index 0f231ef..aa1b225 100644 >>> Binary files a/lib/bio/db/sam/external/libbam.a and b/lib/bio/db/sam/external/libbam.a differ >>> diff --git a/lib/bio/db/sam/library.rb b/lib/bio/db/sam/library.rb >>> index bb78515..e9f8b6e 100644 >>> --- a/lib/bio/db/sam/library.rb >>> +++ b/lib/bio/db/sam/library.rb >>> @@ -9,7 +9,7 @@ module Bio >>> #TODO refactor this piece of code in all the files >>> lib_os = case RUBY_PLATFORM >>> when /linux/ >>> - 'a' >>> + 'so.1' >>> when /darwin/ >>> 'dylib' >>> when /windows/ >>> @@ -22,4 +22,4 @@ module Bio >>> end #Library >>> end #Sam >>> end #DB >>> -end #Bio >>> \ No newline at end of file >>> +end #Bio >>> ------------CUT >>> >>> Then finally reached this state >>> >>> $ ~/ruby192p136/bin/rake >>> (in /home/tomoaki/bioruby-samtools) >>> /home/tomoaki/ruby192p136/bin/ruby -I"lib:lib:test" "/home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" >>> Loaded suite /home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader >>> Started >>> F >>> Finished in 0.000321 seconds. >>> >>> 1) Failure: >>> test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: >>> hey buddy, you should probably rename this file and start testing for real >>> >>> Loading seems ok. >>> I'm not sure if this is bad or ok. >>> >>> Best regards >>> -- >>> Tomoaki NISHIYAMA >>> >>> Advanced Science Research Center, >>> Kanazawa University, >>> 13-1 Takara-machi, >>> Kanazawa, 920-0934, Japan >>> >>> >>> On 2011/02/03, at 17:16, Michal wrote: >>> >>>> Dear Raoul, >>>> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way: >>>> $ tar xvfz ruby-1.9.2-p136.tar.gz >>>> $ cd ruby-1.9.2-p136/ >>>> $ ./configure --prefix=/home/mictadlo/apps/ruby >>>> $ make >>>> $ make install >>>> $ vim ~/.bashrc >>>> export APPS=/home/mictadlo/apps >>>> export RUBY_HOME=$APPS/ruby >>>> export LD_LIBRARY_PATH=/RUBY_HOME/lib >>>> PATH=$RUBY_HOME/bin:$PATH >>>> $ . ~/.bashrc >>>> $ ruby -v >>>> ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux] >>>> >>>> $ gem install ffi >>>> Building native extensions. This could take a while... >>>> Successfully installed ffi-1.0.5 >>>> 1 gem installed >>>> Installing ri documentation for ffi-1.0.5... >>>> Installing RDoc documentation for ffi-1.0.5... >>>> >>>> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git >>>> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/ >>>> remote: Counting objects: 92, done. >>>> remote: Compressing objects: 100% (84/84), done. >>>> remote: Total 92 (delta 21), reused 0 (delta 0) >>>> Unpacking objects: 100% (92/92), done. >>>> >>>> ~/Downloads/git/bioruby-samtools$ rake test >>>> (in /home/mictadlo/Downloads/git/bioruby-samtools) >>>> rake aborted! >>>> no such file to load -- bundler >>>> :29:in `require' >>>> :29:in `require' >>>> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile' >>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run' >>>> /home/mictadlo/apps/ruby/bin/rake:31:in `
' >>>> >>>> What did I wrong? >>>> >>>> Thank you in advance. >>>> >>>> Michal >>>> >>>> On 01/31/2011 08:11 PM, Raoul Bonnal wrote: >>>>> Dear Michal, >>>>> please check this out: >>>>> >>>>> https://github.com/helios/bioruby-samtools >>>>> >>>>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows. >>>>> I need to test the linux library because I'm developing under osx. >>>>> If the libbam.a is wrong please give me the right one and I'll add it to the repo. >>>>> Also note that the library has been compiled for 64bit. >>>>> >>>>> Ciao! >>>>> >>>>> On 30/gen/2011, at 12.42, Michal wrote: >>>>> >>>>>> Hi, >>>>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response. >>>>>> >>>>>> What did I wrong? >>>>>> >>>>>> Michal >>>>>> _______________________________________________ >>>>>> BioRuby Project - http://www.bioruby.org/ >>>>>> BioRuby mailing list >>>>>> BioRuby at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>>> -- >>>>> R.J.P.B. >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >> -- >> R.J.P.B. >> >> >> >> >> > > -- R.J.P.B. From mictadlo at gmail.com Fri Feb 4 11:25:54 2011 From: mictadlo at gmail.com (Michal) Date: Fri, 04 Feb 2011 21:25:54 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> Message-ID: <4D4BE242.2030408@gmail.com> Hi, I have tried the svn version and I have got the following error: ~/Downloads/svn/ $ svn co https://samtools.svn.sourceforge.net/svnroot/samtools samtools Checked out revision 910. ~/Downloads/svn/samtools/trunk/samtools$ make dylib ~/Downloads/svn/samtools/trunk/samtools$ cp libbam.so.1 ~/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/ ~/Downloads/svn/samtools/trunk/samtools$ cd ~/Downloads/git/bioruby-samtools ~/Downloads/git/bioruby-samtools$ rake test (in /home/mictadlo/Downloads/git/bioruby-samtools) /home/mictadlo/apps/ruby/bin/ruby -I"lib:lib:test" "/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb" Loaded suite /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader Started F Finished in 0.000371 seconds. 1) Failure: test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: hey buddy, you should probably rename this file and start testing for real 1 tests, 1 assertions, 1 failures, 0 errors, 0 skips Test run options: --seed 16981 rake aborted! Command failed with status (1): [/home/mictadlo/apps/ruby/bin/ruby -I"lib:l...] /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:993:in `block in sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `sh' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1027:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `ruby' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:115:in `block (2 levels) in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1110:in `verbose' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:100:in `block in define' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `call' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `block in execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `execute' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:595:in `block in invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/monitor.rb:201:in `mon_synchronize' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:588:in `invoke_with_call_chain' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:581:in `invoke' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2041:in `invoke_task' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block (2 levels) in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `each' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block in top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2013:in `top_level' /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1992:in `run' /home/mictadlo/apps/ruby/bin/rake:31:in `
' ~/Downloads/git/bioruby-samtools$ I understand how difficult it is to keep track and it is a good idea to ship bioruby-samtools with a working samtools version like Raoul does it. What I have forgotten to do? Thank you in advance. Michal On 02/04/2011 06:31 PM, Tomoaki NISHIYAMA wrote: > Hi, > >> ~/Downloads/samtools-0.1.12a > > The *latest* samtools which I used was r910 via svn yesterday. > r854 produced the same error as you have shown. > > Samtools is under very active development, as seen from the mailing > list flow. > So, some change in the samtools code made this difference, > and its a bit difficult to keep track with all the update. > > -- > > Tomoaki NISHIYAMA > > > Advanced Science Research Center, > > Kanazawa University, > > 13-1 Takara-machi, > > Kanazawa, 920-0934, Japan > > > From tomoakin at kenroku.kanazawa-u.ac.jp Fri Feb 4 12:26:24 2011 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Fri, 4 Feb 2011 21:26:24 +0900 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4BE242.2030408@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> <4D4BE242.2030408@gmail.com> Message-ID: Hi, > What I have forgotten to do? Now, you are at the point I reached yesterday and I don't think you have forgotten anything. From yesterday's mail: > 1) Failure: > test: BioSamtools should probably rename this file and start > testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: > hey buddy, you should probably rename this file and start testing > for real > > Loading seems ok. > I'm not sure if this is bad or ok. You could look at test/test_bio-samtools.rb $ cat test/test_bio-samtools.rb require 'helper' class TestBioSamtools < Test::Unit::TestCase should "probably rename this file and start testing for real" do flunk "hey buddy, you should probably rename this file and start testing for real" end end and guess what it means. My guess is that this is test not implemented yet. So, this error does not tell if the library function well or can not used at all. You might just try what you wanted to do and see if it works. > I understand how difficult it is to keep track and it is a good > idea to ship bioruby-samtools > with a working samtools version like Raoul does it. My view is the opposite. Since it potentially has many bugs and changes rapidly, bundled shipping is ineffective. With the lack of test code, we cannot even tell which is a good working version. -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan From mictadlo at gmail.com Fri Feb 4 13:13:33 2011 From: mictadlo at gmail.com (Michal) Date: Fri, 04 Feb 2011 23:13:33 +1000 Subject: [BioRuby] samtools-ruby In-Reply-To: References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> <4D4BE242.2030408@gmail.com> Message-ID: <4D4BFB7D.9070004@gmail.com> Hi, I would be happy if would find out how to get on a particular position the alignment and then I could give feedback. Pysam http://code.google.com/p/pysam/ contains all files and tests. ~/Downloads/pysam-0.3.1/tests$ ls 00README.txt ex4.sam ex8.sam Makefile ex1.fa ex5.sam example.gtf.gz pysam_test.py ex1.sam.gz ex6.sam example.gtf.gz.tbi segfault_tests.py ex3.sam ex7.sam example.py tabix_test.py Maybe it would be possible to test bioruby-samtools in the same way. Pysam is ship out with samtools source code and maybe could be used it for bioruby-samtools. Thank you in advance. Michal On 02/04/2011 10:26 PM, Tomoaki NISHIYAMA wrote: > Hi, > >> What I have forgotten to do? > > Now, you are at the point I reached yesterday and > I don't think you have forgotten anything. > > From yesterday's mail: >> 1) Failure: >> test: BioSamtools should probably rename this file and start testing >> for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: >> hey buddy, you should probably rename this file and start testing for >> real >> >> Loading seems ok. >> I'm not sure if this is bad or ok. > > You could look at test/test_bio-samtools.rb > $ cat test/test_bio-samtools.rb > require 'helper' > > class TestBioSamtools < Test::Unit::TestCase > should "probably rename this file and start testing for real" do > flunk "hey buddy, you should probably rename this file and start > testing for real" > end > end > > and guess what it means. > > My guess is that this is test not implemented yet. > So, this error does not tell if the library function well or can not > used at all. > You might just try what you wanted to do and see if it works. > >> I understand how difficult it is to keep track and it is a good idea >> to ship bioruby-samtools >> with a working samtools version like Raoul does it. > > My view is the opposite. > Since it potentially has many bugs and changes rapidly, bundled > shipping is ineffective. > With the lack of test code, we cannot even tell which is a good > working version. > > -- > > Tomoaki NISHIYAMA > > > Advanced Science Research Center, > > Kanazawa University, > > 13-1 Takara-machi, > > Kanazawa, 920-0934, Japan > > From bonnalraoul at ingm.it Fri Feb 4 13:57:07 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 4 Feb 2011 14:57:07 +0100 Subject: [BioRuby] samtools-ruby In-Reply-To: <4D4BFB7D.9070004@gmail.com> References: <4D454E91.1080604@gmail.com> <4D4A6459.5050205@gmail.com> <5B31A257-DDCB-4BBB-A201-B4D708E82BE0@kenroku.kanazawa-u.ac.jp> <4D4BB255.7030703@gmail.com> <4D4BE242.2030408@gmail.com> <4D4BFB7D.9070004@gmail.com> Message-ID: <74EAEDFF-D8D0-42E0-93B8-51C4986CEC65@ingm.it> In these days, w.e. too, I have no time for sam tools. From the next week I could spend more time on this project and improve test, usability and platform supports. On 04/feb/2011, at 14.13, Michal wrote: > Hi, > I would be happy if would find out how to get on a particular position the alignment and then I could give feedback. > > Pysam http://code.google.com/p/pysam/ contains all files and tests. > ~/Downloads/pysam-0.3.1/tests$ ls > 00README.txt ex4.sam ex8.sam Makefile > ex1.fa ex5.sam example.gtf.gz pysam_test.py > ex1.sam.gz ex6.sam example.gtf.gz.tbi segfault_tests.py > ex3.sam ex7.sam example.py tabix_test.py > > Maybe it would be possible to test bioruby-samtools in the same way. Pysam is ship out with samtools source code and maybe could be used it for bioruby-samtools. > > Thank you in advance. > > Michal > > > On 02/04/2011 10:26 PM, Tomoaki NISHIYAMA wrote: >> >> Hi, >> >>> What I have forgotten to do? >> >> Now, you are at the point I reached yesterday and >> I don't think you have forgotten anything. >> >> From yesterday's mail: >>> 1) Failure: >>> test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]: >>> hey buddy, you should probably rename this file and start testing for real >>> >>> Loading seems ok. >>> I'm not sure if this is bad or ok. >> >> You could look at test/test_bio-samtools.rb >> $ cat test/test_bio-samtools.rb >> require 'helper' >> >> class TestBioSamtools < Test::Unit::TestCase >> should "probably rename this file and start testing for real" do >> flunk "hey buddy, you should probably rename this file and start testing for real" >> end >> end >> >> and guess what it means. >> >> My guess is that this is test not implemented yet. >> So, this error does not tell if the library function well or can not used at all. >> You might just try what you wanted to do and see if it works. >> >>> I understand how difficult it is to keep track and it is a good idea to ship bioruby-samtools >>> with a working samtools version like Raoul does it. >> >> >> My view is the opposite. >> Since it potentially has many bugs and changes rapidly, bundled shipping is ineffective. >> With the lack of test code, we cannot even tell which is a good working version. >> -- >> Tomoaki NISHIYAMA >> >> Advanced Science Research Center, >> Kanazawa University, >> 13-1 Takara-machi, >> Kanazawa, 920-0934, Japan >> > -- R.J.P.B. From hlapp at drycafe.net Sat Feb 5 23:45:47 2011 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 5 Feb 2011 18:45:47 -0500 Subject: [BioRuby] NESCent Seeks Hackathon Whitepapers In-Reply-To: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> References: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> Message-ID: <066A2391-6041-408C-B26E-9B867DE785C7@drycafe.net> The National Evolutionary Synthesis Center (NESCent), in keeping with its objective to promote collaborative development of open-source, reusable, and standards-supporting informatics resources, sponsors highly collaborative, face-to-face software development events, called "hackathons" (see [1]). To ensure that this program continues to be responsive to user needs and to tap into the expertise and creativity of the evolutionary biology community, NESCent is soliciting short whitepapers (2-6 pages) [2] on potential target areas for future hackathons. To further encourage submissions, we have now distilled specific guidelines for proposing hackathon events, based on the experiences gained from events we have sponsored in the past: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines The Center's Call for Informatics Whitepapers [3] includes not only hackathons, but also a large spectrum of other initiatives to be undertaken by the Center, including training, software development, collaborative ontology development, and coordination of data standards. Whitepapers are accepted at any time and reviewed on an on- going basis. URLs: [1] Collaborative cyberinfrastructure events and programs organized by NESCent: http://informatics.nescent.org/wiki/Main_Page [2] NESCent Call for Informatics Whitepapers http://www.nescent.org/informatics/whitepapers.php [3] Hackathon Whitepaper Guidelines: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines [4] Past NESCent-sponsored hackathons: http://informatics.nescent.org/wiki/Main_Page#Hackathons From jan.aerts at gmail.com Mon Feb 7 08:42:24 2011 From: jan.aerts at gmail.com (Jan Aerts) Date: Mon, 7 Feb 2011 09:42:24 +0100 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> Message-ID: I've been using rake for my NGS analyses while I still worked at Sanger. Will post more about that in the next couple of days. jan. On 21 December 2010 18:50, Raoul Bonnal wrote: > My original request was on analysis approach on NGS and transcriptome. > > btw > > > Very interesting Hiro, > > searching on github there is also this project: > https://github.com/grosser/parallel > > Run any code in parallel Processes(> use all CPUs) or Threads(> speedup > blocking operations). > Best suited for map-reduce or e.g. parallel downloads/uploads. > Processes > > Speedup through multiple CPUs > Speedup for blocking operations > Protects global data > Extra memory used ( very low on REE through copy_on_write_friendly ) > Child processes are killed when your main process is killed through Ctrl+c > or kill -2 > Threads > > Speedup for blocking operations > Global data can be modified > No extra memory used > Processes/Threads are workers, they grab the next piece of work when they > finish > > > On 21/dic/2010, at 15.29, MISHIMA, Hiroyuki wrote: > > > Hi all, > > > > I would like to say something about workflow automation in Ruby. > > > > Recently I am interested in using Parallel Workflow extention for Rake > > (Pwrake) for NextGen sequencer data processing. As you may know, Rake is > Ruby Make, a build tool. > > > > Pwrake is developped by Masahiro Tanaka at University of Tsukuba. He is > > also the author of "NArray", very fast matrix calculation engine for > > Ruby. Although Pwrake and regular Rake are compatible in syntax, Pwrake > > automatically detects workflow steps that can be run in parallel. > > > > Pwrake's parallelization model is "process based". Because I am just a > > *user* of bioinformatics packages (like BWA/GATK/DINDEL etc..), it is > > what I need. > > > > Pwrake invokes processes via ssh and supports the Gfarm large-scale > > distributed filesystem. Of course, it works well on a multi-processor > > Linux box. > > > > Although Pwrake is developed for astronomy science, its goal is also > > common in bioinformatics. > > > > I think that some helper methods may simplify Rakefiles for > bioinformatics, and such helper methods are good for a BioRuby plugin. > > > > FYI, > > Pwrake on github: > > https://github.com/masa16/Pwrake/ > > > > Presentation at RubyConfX: > > http://www.slideshare.net/masa16tanaka/ruby-conftanaka16 > > > > Presentation at PRAGMA18: > > http://goc.pragma-grid.net/pragma-doc/pragma18/Cool_Things/pwrake.pptx > > > > Thanks, > > Hiro. > > > > Raoul Bonnal wrote(2010/12/21 21:33): > >> Hi all, I read in the irc's log that a lot of the memebers are or > >> will start working on ngs data. I'll re-start ( I worked on 454) with > >> the Illumina platform, in few week, do you have some consolidate > >> workflow to follow for transcriptome analysis ? > >> > >> papers, blogs, etc.. everything is ok :-) > >> > >> I'm also interested about the workflow discussion but... are the > >> workflow intended to let the not bioinformaticians analyze complex > >> datasets or automate some tedious and repetitive task that we > >> (bioinformaticians) must do every time ? In both cases our life will > >> be probably better :-) > >> > >> -- Ra > > -- > > MISHIMA, Hiroyuki, DDS, Ph.D. > > COE Research Fellow > > Department of Human Genetics > > Nagasaki University Graduate School of Biomedical Sciences > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From missy at be.to Mon Feb 7 12:32:34 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Mon, 07 Feb 2011 21:32:34 +0900 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> Message-ID: <4D4FE662.3070204@be.to> Hi Jan and all, I am looking forward to hearing from you about your experience on rake and NGS analyses. I have read your blog informative article ( http://saaientist.blogspot.com/ ) about rake for software projects and a GitHub repository BioRake ( https://github.com/jandot/biorake ). BioRake's "event" method is elegant. In my DINDEL workflow rakefile, I use a dummy file as a representative of all dynamically generated intermediate files in Stage 3. The event method may express the logic and simplify the description. Sincerely yours, Hiro. Jan Aerts wrote (2011/02/07 17:42): > I've been using rake for my NGS analyses while I still worked at > Sanger. Will post more about that in the next couple of days. > > jan. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From pjotr.public14 at thebird.nl Mon Feb 7 17:16:55 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 7 Feb 2011 18:16:55 +0100 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> Message-ID: <20110207171655.GA25517@thebird.nl> On Mon, Feb 07, 2011 at 09:42:24AM +0100, Jan Aerts wrote: > I've been using rake for my NGS analyses while I still worked at Sanger. > Will post more about that in the next couple of days. It is interesting to integrate it with rq - which can parallelize calculations with zero-administration (all that is needed is a shared dir). I kinda 'inherited' the project, and introduced a few bugs, see https://github.com/pjotrp/rq It will soon have a debian package. Pj. From missy at be.to Tue Feb 8 01:06:57 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Tue, 08 Feb 2011 10:06:57 +0900 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: <20110207171655.GA25517@thebird.nl> References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> <20110207171655.GA25517@thebird.nl> Message-ID: <4D509731.4050209@be.to> Hi, I added Pjotr's information on the BioRuby wiki ( http://bioruby.open-bio.org/wiki/Workflows ). I also updated a subsection about GridEngine. Univa took over GridEngine development from Oracle. Sincerely yours, Hiro. Pjotr Prins wrote (2011/02/08 2:16): > rq - which can parallelize calculations with zero-administration > (all that is needed is a shared dir). -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From bonnalraoul at ingm.it Wed Feb 9 11:58:50 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 9 Feb 2011 12:58:50 +0100 Subject: [BioRuby] Workflows and Parallelization In-Reply-To: <4D509731.4050209@be.to> References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> <20110207171655.GA25517@thebird.nl> <4D509731.4050209@be.to> Message-ID: <97CFB702-337B-4608-8AF5-CADAB7B1702A@ingm.it> Hello folks, tweeting around I found these videos http://www.youtube.com/watch?v=1ntxT-47VPA http://www.youtube.com/watch?v=OpaiGYxkSuQ&feature=related http://www.youtube.com/watch?v=P40akGWJ_gY&feature=related Project home page: http://www.gnu.org/software/parallel/ Very useful in many contexts. @BioRuby: I think that we can explore how to use it in workflows. On 08/feb/2011, at 02.06, MISHIMA, Hiroyuki wrote: > Hi, > > I added Pjotr's information on the BioRuby wiki > ( http://bioruby.open-bio.org/wiki/Workflows ). > > I also updated a subsection about GridEngine. Univa took over GridEngine > development from Oracle. > > Sincerely yours, > Hiro. > > Pjotr Prins wrote (2011/02/08 2:16): >> rq - which can parallelize calculations with zero-administration >> (all that is needed is a shared dir). > > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra From francesco.strozzi at gmail.com Wed Feb 9 13:13:00 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Wed, 9 Feb 2011 14:13:00 +0100 Subject: [BioRuby] Bio::BWA Message-ID: Hi all, the version 0.1 of the BWA Plugin is now available for tests! The code is at https://github.com/fstrozzi/bioruby-bwa Details on this plugin with some examples are available at https://github.com/fstrozzi/bioruby-bwa/wiki Plugin documentation is available at http://fstrozzi.github.com/bioruby-bwa/ The plugin runs with ruby-ffi and includes two pre-compiled BWA shared libraries for Linux and Mac OS X (64bit only). I've run tests on both systems and the results are fine. For what I have seen the plugin works with the same performance as the standalone BWA (I will add details on the benchmarks to the wiki asap). Before releasing a gem I would like more tests from someone else other than me ;-). Particularly to check if the pre-compiled libraries works fine or if there are issues here and there. So please checkout the code, try it and let me know your feedbacks! Thanks and cheers -- Francesco From missy at be.to Thu Feb 10 04:59:42 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Thu, 10 Feb 2011 13:59:42 +0900 Subject: [BioRuby] Spamming on the BioRuby wiki Message-ID: <4D5370BE.3050407@be.to> Hi, Recently, I found spamming on the BioRuby wiki. Many user accounts and spam articles seem to be created automatically. Does anyone know good ways to prevent such activities? Sincerely yours, Hiro -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From ktym at hgc.jp Thu Feb 10 05:32:53 2011 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu, 10 Feb 2011 14:32:53 +0900 Subject: [BioRuby] Spamming on the BioRuby wiki In-Reply-To: <4D5370BE.3050407@be.to> References: <4D5370BE.3050407@be.to> Message-ID: Hi Hiro, Thank you for your notification and deletion of spam texts. We had a similar problem few months ago but it occurred again, very sad. We don't want to waste our time for reverting those wiki pages anymore, I'll ask OBF staff to require authorization before creating new account. Judged from current usage of the wiki and the size of our community, I think this change won't spoil our activity. Toshiaki On 2011/02/10, at 13:59, MISHIMA, Hiroyuki wrote: > Hi, > > Recently, I found spamming on the BioRuby wiki. Many user accounts and > spam articles seem to be created automatically. > > Does anyone know good ways to prevent such activities? > > Sincerely yours, > Hiro > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From cjfields at illinois.edu Thu Feb 10 14:26:52 2011 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 10 Feb 2011 08:26:52 -0600 Subject: [BioRuby] Spamming on the BioRuby wiki In-Reply-To: References: <4D5370BE.3050407@be.to> Message-ID: <2820FD5F-A103-480C-9E78-BD172A7F169E@illinois.edu> This has been happening across all the OBF wikis unfortunately. I think Jason is adding a ReCaptcha system for bioperl.org, might be a good idea to do the same for bioruby. chris On Feb 9, 2011, at 11:32 PM, Toshiaki Katayama wrote: > Hi Hiro, > > Thank you for your notification and deletion of spam texts. > We had a similar problem few months ago but it occurred again, very sad. > > We don't want to waste our time for reverting those wiki pages anymore, > I'll ask OBF staff to require authorization before creating new account. > Judged from current usage of the wiki and the size of our community, > I think this change won't spoil our activity. > > Toshiaki > > > On 2011/02/10, at 13:59, MISHIMA, Hiroyuki wrote: > >> Hi, >> >> Recently, I found spamming on the BioRuby wiki. Many user accounts and >> spam articles seem to be created automatically. >> >> Does anyone know good ways to prevent such activities? >> >> Sincerely yours, >> Hiro >> -- >> MISHIMA, Hiroyuki, DDS, Ph.D. >> COE Research Fellow >> Department of Human Genetics >> Nagasaki University Graduate School of Biomedical Sciences >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From mikeco57 at gmail.com Thu Feb 10 18:29:07 2011 From: mikeco57 at gmail.com (Michael O'Keefe) Date: Thu, 10 Feb 2011 13:29:07 -0500 Subject: [BioRuby] Contributing Message-ID: <4D542E73.5060708@gmail.com> Hello everyone, My name is Michael O'Keefe. I am a student in bioinformatics at Rensselaer Polytechnic Institute, and I am participating in a group that sponsors work on open-source projects ( rcos.cs.rpi.edu ). I would like to contribute to BioRuby, and would like to know where the best place to start is. Is there a specific part of the project that I could work on? I wouldn't mind working on bugfixes, or any other project that could use some work. Thank you very much, Michael O'Keefe mikeco57 at gmail.com From p.j.a.cock at googlemail.com Sat Feb 12 00:12:06 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 12 Feb 2011 00:12:06 +0000 Subject: [BioRuby] Spamming on the BioRuby wiki In-Reply-To: <2820FD5F-A103-480C-9E78-BD172A7F169E@illinois.edu> References: <4D5370BE.3050407@be.to> <2820FD5F-A103-480C-9E78-BD172A7F169E@illinois.edu> Message-ID: On Thu, Feb 10, 2011 at 2:26 PM, Chris Fields wrote: > This has been happening across all the OBF wikis unfortunately. >?I think Jason is adding a ReCaptcha system for bioperl.org, > might be a good idea to do the same for bioruby. > > chris Hi Chris, I hope the ReCaptcha system works and can be applied to all the OBF wikis. If it doesn't stop the spam, I think the suggestion that account creation should require manual authorisation is a good idea - certainly on Biopython the number of real wiki account requests is low. Peter From cjfields at illinois.edu Sat Feb 12 01:29:59 2011 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 11 Feb 2011 19:29:59 -0600 Subject: [BioRuby] Spamming on the BioRuby wiki In-Reply-To: References: <4D5370BE.3050407@be.to> <2820FD5F-A103-480C-9E78-BD172A7F169E@illinois.edu> Message-ID: <740EE9EF-458F-45BF-B8AF-641CAC292BB7@illinois.edu> On Feb 11, 2011, at 6:12 PM, Peter Cock wrote: > On Thu, Feb 10, 2011 at 2:26 PM, Chris Fields wrote: >> This has been happening across all the OBF wikis unfortunately. >> I think Jason is adding a ReCaptcha system for bioperl.org, >> might be a good idea to do the same for bioruby. >> >> chris > > Hi Chris, > > I hope the ReCaptcha system works and can be applied > to all the OBF wikis. If it doesn't stop the spam, I think > the suggestion that account creation should require manual > authorisation is a good idea - certainly on Biopython the > number of real wiki account requests is low. > > Peter We can switch to that if needed. Jason had problems getting ReCaptcha working, but I may take a crack at it before we move to a manual system (which may be more of a pain, considering how many spam requests might be made). chris From pjotr.public14 at thebird.nl Mon Feb 14 14:46:39 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 14 Feb 2011 15:46:39 +0100 Subject: [BioRuby] Plugins, Biogem and Christmas 2010 In-Reply-To: <3F1D10FB-B121-4819-A519-87A6637DD8F6@ingm.it> References: <3F1D10FB-B121-4819-A519-87A6637DD8F6@ingm.it> Message-ID: <20110214144639.GA26838@thebird.nl> Yet another BioRuby plugin. I just released a fast BLAST XML file parser for big data (i.e. it does not necessarily load everything in memory). It is based on Nokogiri+libxml2. A quick test shows it is 50x faster than the ReXML parser that comes with BioRuby. Install with gem install bio-blastxmlparse It comes with a utility to produce tabular output blastxmlparser --help Docs at https://github.com/pjotrp/blastxmlparser (you may need to install libxml2-dev first, to build the native extension). There is a choice of two parsers, loading the DOM in memory, or split the XML file in smaller sections. I ran quite a few test to see what type of parsing would give best results. Currently I parse the DOM, walk the low level nodes, and use (lazy) XPath for the values. There is probably still room for improvement. One thing I will still try, when I have time, is parallelized parsing on JRuby. With that it should be one of the fastest BLAST parsers on the planet. Enjoy, Pj. On Fri, Dec 24, 2010 at 12:08:04PM +0100, Raoul Bonnal wrote: > BioRuby plugin system was firstly announced at [BOSC 2010] and will be implemented by the Christmas 2010. Hopefully. :) -- Yes, we made it! Check out the BiogemInstallation and BiogemDevelopment sections. From pjotr.public14 at thebird.nl Tue Feb 15 08:14:57 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 15 Feb 2011 09:14:57 +0100 Subject: [BioRuby] Plugins, Biogem and Christmas 2010 In-Reply-To: <20110214144639.GA26838@thebird.nl> References: <3F1D10FB-B121-4819-A519-87A6637DD8F6@ingm.it> <20110214144639.GA26838@thebird.nl> Message-ID: <20110215081457.GA30678@thebird.nl> At this point bio-blastxmlparse works on Ruby 1.9 only. It should be possible to use Enumerator on 1.8 - I'll look into that at some point. Pj. From bonnalraoul at ingm.it Tue Feb 15 09:37:36 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Tue, 15 Feb 2011 10:37:36 +0100 Subject: [BioRuby] SRA downloader Message-ID: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> Hey Guys, this is a new plugin to download sra archives in an easy way, I hope :-) Why ? because I need to download some file from SRA and I don't want to type the wget/curl command and I want to explore the ftp from command line, then because I need to start the downloads in background on a remote server. Where ? https://github.com/helios/bioruby-sradl as usual is experimental so, please be careful. I'm quite lazy so test section doesn't exist and the code needs some refactoring; I know I'll add it soon. The DSL needs to be improved. The procedure is recursive so you can download a bunch of reads at the same time. By default the reads downloaded are the LITE. In the read me there is an example of looking for a regular archive: it's also an example of using optional parameters in thor' scripts. To post process SRA format you need the sra tools kit http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.3_Installing_the_Too This plugin has also the purpose to be demonstrative for a Thor application. This could be added to our NGS ngs section. Any suggestion is welcome. Ciao. -- Ra From bonnalraoul at ingm.it Tue Feb 15 10:25:26 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Tue, 15 Feb 2011 11:25:26 +0100 Subject: [BioRuby] SRA downloader In-Reply-To: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> Message-ID: <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> Next time a little bit of research :-( http://phylogenomics.blogspot.com/2011/02/though-i-generally-love-ncbi.html?showComment=1297359206321#c7246439301219289057 On 15/feb/2011, at 10.37, Raoul Bonnal wrote: > Hey Guys, > this is a new plugin to download sra archives in an easy way, I hope :-) > > Why ? because I need to download some file from SRA and I don't want to type the wget/curl command and I want to explore the ftp from command line, then because I need to start the downloads in background on a remote server. > > Where ? https://github.com/helios/bioruby-sradl > > as usual is experimental so, please be careful. I'm quite lazy so test section doesn't exist and the code needs some refactoring; I know I'll add it soon. > The DSL needs to be improved. > > The procedure is recursive so you can download a bunch of reads at the same time. > > By default the reads downloaded are the LITE. In the read me there is an example of looking for a regular archive: it's also an example of using optional parameters in thor' scripts. > To post process SRA format you need the sra tools kit > > http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.3_Installing_the_Too > > This plugin has also the purpose to be demonstrative for a Thor application. > > This could be added to our NGS ngs section. > > Any suggestion is welcome. > > Ciao. > -- > Ra > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra From p.j.a.cock at googlemail.com Tue Feb 15 13:18:47 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 15 Feb 2011 13:18:47 +0000 Subject: [BioRuby] SRA downloader In-Reply-To: <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> Message-ID: On Tue, Feb 15, 2011 at 10:25 AM, Raoul Bonnal wrote: > Next time a little bit of research ?:-( > > http://phylogenomics.blogspot.com/2011/02/though-i-generally-love-ncbi.html?showComment=1297359206321#c7246439301219289057 > Still no official announcement yet though... > On 15/feb/2011, at 10.37, Raoul Bonnal wrote: > >> Hey Guys, >> this is a new plugin to download sra archives in an easy way, I hope :-) >> >> Why ? because I need to download some file from SRA and I don't want >> to type the wget/curl command and I want to explore the ftp from command >> line, then because I need to start the downloads in background on a remote >> server. >> You might be interested in this solution too, http://fungalgenomes.org/blog/2011/02/a-hyphaltip-get-a-bunch-of-sra-data/ Peter From bonnalraoul at ingm.it Tue Feb 15 13:45:09 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Tue, 15 Feb 2011 14:45:09 +0100 Subject: [BioRuby] SRA downloader In-Reply-To: References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> Message-ID: <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> Hi Peter, On 15/feb/2011, at 14.18, Peter Cock wrote: > http://fungalgenomes.org/blog/2011/02/a-hyphaltip-get-a-bunch-of-sra-data/ thanks for the link. Actually, DDBJ and EBI (ENA) have a repository for SRA datasets. The question is? Do we need to support SRA or it's just a convenient way for providers to store data? EBI seems to me more computer friendly than NIH site. If more providers will switch to Aspera, there is a developer kit SDK http://www.asperasoft.com/en/products/fasp_SDK_9/fasp_SDK_9 that could be interesting to support. Today I tested the download speed and it performs very well compared to normal ftp. -- Ra From cjfields at illinois.edu Tue Feb 15 14:57:17 2011 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 15 Feb 2011 08:57:17 -0600 Subject: [BioRuby] SRA downloader In-Reply-To: <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> Message-ID: <62BA7169-FB1F-42E6-AD8B-16BEC9E356E4@illinois.edu> On Feb 15, 2011, at 7:45 AM, Raoul Bonnal wrote: > Hi Peter, > On 15/feb/2011, at 14.18, Peter Cock wrote: > >> http://fungalgenomes.org/blog/2011/02/a-hyphaltip-get-a-bunch-of-sra-data/ > thanks for the link. > > Actually, DDBJ and EBI (ENA) have a repository for SRA datasets. > The question is? Do we need to support SRA or it's just a convenient way for providers to store data? Yes, I think there needs to be support for easier data retrieval, but of course only if there will be a SRA database to being with. All the feedback (both positive and negative) from Eisen's blog indicates the need for such a resource, albeit with an improved UI. Unfortunately, the most significant problem we're seeing on the NCBI end is (I believe) a general lack of funding for on-going and new projects; this has been going on for a while now. As Peter pointed out removal of SRA and other resources hasn't been made official (the link quotes an anonymous source). However, past cuts at NCBI and the newly released federal budget doesn't make me think there will be a stop gap to prevent SRA and other NCBI resources from going away. > EBI seems to me more computer friendly than NIH site. I generally find the same. > If more providers will switch to Aspera, there is a developer kit SDK http://www.asperasoft.com/en/products/fasp_SDK_9/fasp_SDK_9 that could be interesting to support. > > Today I tested the download speed and it performs very well compared to normal ftp. > > -- > Ra A bit confused on this last part. If we're talking about a simple ftp-like resource to pull data from then I would suggest biotorrents, which is specifically developed for handling large datasets. However, a gzipped blob with an accession is useless without a way to add additional meta-information about it (species, source, protocols, etc etc) and a way to search through such information. Most users will want a searchable and possibly curated repository to pull data from, or at least one that gives them accessions and links to such. There is a need for something like SRA whether NCBI or others decide to handle it. chris From francesco.strozzi at gmail.com Tue Feb 15 16:09:36 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Tue, 15 Feb 2011 17:09:36 +0100 Subject: [BioRuby] bioruby sff reader Message-ID: Hi all, is there a SFF reader to parse 454 output in Ruby? Or is someone working on this? It will be nice to have something like python sff-extract which can read the SFF format and generate ad hoc files like FastQ or Fasta, Qual and XML traceinfo. Bye -- Francesco From p.j.a.cock at googlemail.com Tue Feb 15 16:53:03 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 15 Feb 2011 16:53:03 +0000 Subject: [BioRuby] bioruby sff reader In-Reply-To: References: Message-ID: On Tue, Feb 15, 2011 at 4:09 PM, Francesco Strozzi wrote: > Hi all, > is there a SFF reader to parse 454 output in Ruby? Or is someone working on > this? > It will be nice to have something like python sff-extract which can read the > SFF format and generate ad hoc files like FastQ or Fasta, Qual and XML > traceinfo. If all you want to to convert SFF to FASTQ or FASTA+QUAL plus perhaps the NCBI XML traceinfo why not just use the sff_extract.py script? On the other hand, I can see the utlity in native support for SFF files in (Bio)Ruby. Biopython does this already and there has been some work towards this for BioPerl and BioJava too: http://lists.open-bio.org/pipermail/bioperl-l/2010-November/034223.html http://lists.open-bio.org/pipermail/biojava-dev/2010-November/004451.html Please feel free to look at the Biopython SFF code for this. It was originally based on sff_extract for parsing, but extended to also write SFF and handle the (undocumented) Roche index block. I've tried to include enough comments within the code to make it clear, but I'll happily answer technical questions: https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py There are also unit test example files you can use: https://github.com/biopython/biopython/tree/master/Tests/Roche Peter (Biopython) From bonnalraoul at ingm.it Wed Feb 16 10:31:05 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 16 Feb 2011 11:31:05 +0100 Subject: [BioRuby] Contributing In-Reply-To: <4D542E73.5060708@gmail.com> References: <4D542E73.5060708@gmail.com> Message-ID: <3D975070-639D-475C-8DB2-770A3573793D@ingm.it> Dear Michael, thanks for your interest. Why not to join our regular irc meeting tomorrow (CEST time around 15:00) on irc.freenode.net channel #bioruby ? I'm Helius or ilpuccio on chat. Now, we are working on different topics like workflows, ngs and plugins, you are welcome to contribute in any on them. Now I'm here with Francesco and we think that as a new "biorubyer" it would be very useful if you take a look at the tutorial section and verify is there is something that needs improvements or you miss as a beginner. http://bioruby.open-bio.org/wiki/Tutorial In which field of bioinformatics are you working ? PS: Busy days, delay's reason, sorry. On 10/feb/2011, at 19.29, Michael O'Keefe wrote: > Hello everyone, > > My name is Michael O'Keefe. I am a student in bioinformatics at Rensselaer Polytechnic Institute, and I am participating in a group that sponsors work on open-source projects ( rcos.cs.rpi.edu ). I would like to contribute to BioRuby, and would like to know where the best place to start is. Is there a specific part of the project that I could work on? I wouldn't mind working on bugfixes, or any other project that could use some work. > > Thank you very much, > Michael O'Keefe > mikeco57 at gmail.com > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby Ciao. -- Ra From bonnalraoul at ingm.it Fri Feb 18 11:14:47 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 18 Feb 2011 12:14:47 +0100 Subject: [BioRuby] SRA downloader In-Reply-To: <62BA7169-FB1F-42E6-AD8B-16BEC9E356E4@illinois.edu> References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> <62BA7169-FB1F-42E6-AD8B-16BEC9E356E4@illinois.edu> Message-ID: Hi Chris, On 15/feb/2011, at 15.57, Chris Fields wrote: > On Feb 15, 2011, at 7:45 AM, Raoul Bonnal wrote: > >> If more providers will switch to Aspera, there is a developer kit SDK http://www.asperasoft.com/en/products/fasp_SDK_9/fasp_SDK_9 that could be interesting to support. >> >> Today I tested the download speed and it performs very well compared to normal ftp. >> >> -- >> Ra > > A bit confused on this last part. If we're talking about a simple ftp-like resource to pull data from then I would suggest biotorrents, which is specifically developed for handling large datasets. My point was, NCBI and EBI use Aspera, which has a proprietary way to transfer file, you need their client for a fast download... but don't care about that I don't like that approach. Why are they not using torrents ? Which is the sense of biotorrent ? Just share "personal" data or replicate/mirroring other databases ? I must admit that I need just some SRA file for testing tools. I don't think I will download many sra data in the near future, I can wait 50mins using regular ftp. It was more, which is your feeling with sra and your experience. -- Ra From mh6 at sanger.ac.uk Fri Feb 18 11:38:56 2011 From: mh6 at sanger.ac.uk (Michael Paulini) Date: Fri, 18 Feb 2011 11:38:56 +0000 Subject: [BioRuby] SRA downloader In-Reply-To: References: <02B10A6E-5BA1-4653-B133-9C58FDF8CB0E@ingm.it> <0DB4ED33-D49C-4FDF-87A3-9544EF56BB32@ingm.it> <3D6864B8-5087-4EAE-B462-715C2C2865E2@ingm.it> <62BA7169-FB1F-42E6-AD8B-16BEC9E356E4@illinois.edu> Message-ID: <4D5E5A50.1000200@sanger.ac.uk> On 18/02/2011 11:14, Raoul Bonnal wrote: > Hi Chris, > > On 15/feb/2011, at 15.57, Chris Fields wrote: > >> On Feb 15, 2011, at 7:45 AM, Raoul Bonnal wrote: >> >>> If more providers will switch to Aspera, there is a developer kit SDK http://www.asperasoft.com/en/products/fasp_SDK_9/fasp_SDK_9 that could be interesting to support. >>> >>> Today I tested the download speed and it performs very well compared to normal ftp. >>> >>> -- >>> Ra >> A bit confused on this last part. If we're talking about a simple ftp-like resource to pull data from then I would suggest biotorrents, which is specifically developed for handling large datasets. > My point was, NCBI and EBI use Aspera, which has a proprietary way to transfer file, you need their client for a fast download... but don't care about that I don't like that approach. > > Why are they not using torrents ? Which is the sense of biotorrent ? Just share "personal" data or replicate/mirroring other databases ? > > I must admit that I need just some SRA file for testing tools. I don't think I will download many sra data in the near future, I can wait 50mins using regular ftp. > > It was more, which is your feeling with sra and your experience. > > -- > Ra > Hi Ra, from personal experience the word 'bittorrent' does not fly too high with management ... even if used to distributed 20GB+ VM images. After long-winded fights (making sure we were allowed to distribute every single file, by attaching the respective OSS license to them, and getting agreements form our sister sites to seed), we went back to mirror them across a handful FTP sites instead, as it was "decided" that we can't possible use 'File-Sharing Programs'. M /rant_end -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From mail at michaelbarton.me.uk Mon Feb 21 17:06:07 2011 From: mail at michaelbarton.me.uk (Michael Barton) Date: Mon, 21 Feb 2011 12:06:07 -0500 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension Message-ID: <20110221170607.GA14295@Michael-Bartons-MacBook.local> Hi, Does anyone know of a ruby library for doing local and global sequence alignment? I'm interested in performing these kind of alignments in ruby but would prefer not to call command line tools such as EMBOSS. I think it could be useful to have a ruby gem which installs a C-extension for allowing for reasonably fast alignment. A cursory look on pubmed turned these links for C libraries. http://www.ncbi.nlm.nih.gov/pubmed/18959793 http://www.ncbi.nlm.nih.gov/books/NBK7151/ Mike From francesco.strozzi at gmail.com Tue Feb 22 08:58:12 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Tue, 22 Feb 2011 09:58:12 +0100 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110221170607.GA14295@Michael-Bartons-MacBook.local> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> Message-ID: Hi Michael, I have worked on a Ruby binding to the BWA fast mapping software using FFI. With BWA you can run global alignments as well as local alignments with the standard SW algorithm included in BWA. This is not released as a gem yet, as it's still under testing. If you want to check it out and see if it fits for your purpose you can find the code here : https://github.com/fstrozzi/bioruby-bwa The package includes two pre-compiled libraries for Mac OS X and Linux (64bit only). Cheers Francesco On Mon, Feb 21, 2011 at 18:06, Michael Barton wrote: > Hi, > > Does anyone know of a ruby library for doing local and global sequence > alignment? I'm interested in performing these kind of alignments in ruby > but > would prefer not to call command line tools such as EMBOSS. I think it > could be > useful to have a ruby gem which installs a C-extension for allowing for > reasonably fast alignment. A cursory look on pubmed turned these links for > C libraries. > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > Mike > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > -- Francesco From ngoto at gen-info.osaka-u.ac.jp Tue Feb 22 09:11:20 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 22 Feb 2011 18:11:20 +0900 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110221170607.GA14295@Michael-Bartons-MacBook.local> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> Message-ID: <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> Hi, There was SWlib, an implementation of Smith-Waterman algorithm for Ruby. It was written by OKUJI K. Yoshinori in 2001. Since it is very old, some modification would be needed for correct working. http://bioruby.open-bio.org/contrib/swlib/ Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Mon, 21 Feb 2011 12:06:07 -0500 Michael Barton wrote: > Hi, > > Does anyone know of a ruby library for doing local and global sequence > alignment? I'm interested in performing these kind of alignments in ruby but > would prefer not to call command line tools such as EMBOSS. I think it could be > useful to have a ruby gem which installs a C-extension for allowing for > reasonably fast alignment. A cursory look on pubmed turned these links for > C libraries. > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > Mike From mail at michaelbarton.me.uk Tue Feb 22 16:48:21 2011 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 22 Feb 2011 11:48:21 -0500 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20110222164821.GA2096@nku069218.hh.nku.edu> Thank you Naohisa and Francesco for your suggestions. I will try experimenting with these two libraries. I had also just read an interesting article on using C extensions in Ruby which I thought might be of general interest to the mailing list - http://robots.thoughtbot.com/post/1037240922 On Tue, Feb 22, 2011 at 06:11:20PM +0900, Naohisa GOTO wrote: > Hi, > > There was SWlib, an implementation of Smith-Waterman algorithm for Ruby. It > was written by OKUJI K. Yoshinori in 2001. Since it is very old, some > modification would be needed for correct working. > http://bioruby.open-bio.org/contrib/swlib/ > > Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > On Mon, 21 Feb 2011 12:06:07 -0500 Michael Barton > wrote: > > > Hi, > > > > Does anyone know of a ruby library for doing local and global sequence > > alignment? I'm interested in performing these kind of alignments in ruby > > but would prefer not to call command line tools such as EMBOSS. I think it > > could be useful to have a ruby gem which installs a C-extension for > > allowing for reasonably fast alignment. A cursory look on pubmed turned > > these links for C libraries. > > > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > > > Mike > > _______________________________________________ BioRuby Project > - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnalraoul at ingm.it Tue Feb 22 18:36:36 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Tue, 22 Feb 2011 19:36:36 +0100 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222164821.GA2096@nku069218.hh.nku.edu> Message-ID: <20110222183636.8da2b75f@mail.ingm.it> Hi Michael, thanks for the post. Why not open a Geek section on the wiki for this type of links ? _____ From: Michael Barton [mailto:mail at michaelbarton.me.uk] To: BioRuby Mailing List [mailto:bioruby at lists.open-bio.org] Sent: Tue, 22 Feb 2011 17:48:21 +0100 Subject: Re: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension Thank you Naohisa and Francesco for your suggestions. I will try experimenting with these two libraries. I had also just read an interesting article on using C extensions in Ruby which I thought might be of general interest to the mailing list - http://robots.thoughtbot.com/post/1037240922 On Tue, Feb 22, 2011 at 06:11:20PM +0900, Naohisa GOTO wrote: > Hi, > > There was SWlib, an implementation of Smith-Waterman algorithm for Ruby. It > was written by OKUJI K. Yoshinori in 2001. Since it is very old, some > modification would be needed for correct working. > http://bioruby.open-bio.org/contrib/swlib/ > > Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > On Mon, 21 Feb 2011 12:06:07 -0500 Michael Barton > wrote: > > > Hi, > > > > Does anyone know of a ruby library for doing local and global sequence > > alignment? I'm interested in performing these kind of alignments in ruby > > but would prefer not to call command line tools such as EMBOSS. I think it > > could be useful to have a ruby gem which installs a C-extension for > > allowing for reasonably fast alignment. A cursory look on pubmed turned > > these links for C libraries. > > > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > > > Mike > > _______________________________________________ BioRuby Project > - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Tue Feb 22 18:47:41 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 22 Feb 2011 19:47:41 +0100 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222164821.GA2096@nku069218.hh.nku.edu> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> <20110222164821.GA2096@nku069218.hh.nku.edu> Message-ID: <20110222184741.GA21681@thebird.nl> On Tue, Feb 22, 2011 at 11:48:21AM -0500, Michael Barton wrote: > Thank you Naohisa and Francesco for your suggestions. I will try experimenting > with these two libraries. I had also just read an interesting article on using > C extensions in Ruby which I thought might be of general interest to the > mailing list - > > http://robots.thoughtbot.com/post/1037240922 This discusses using a Ruby C interface. Note: it is not the easiest way. Especially with existing C libs you may be better off with FFI or SWIG. The first makes mapping to Ruby easy, the second maps to all languages. For most Ruby bindings FFI is preferred, also because it does JRuby. Binding existing libraries is usually non-trivial. Because C has no GC, and buffers get passed around as function parameters. Pj. From mail at michaelbarton.me.uk Tue Feb 22 19:43:09 2011 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 22 Feb 2011 14:43:09 -0500 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222184741.GA21681@thebird.nl> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> <20110222164821.GA2096@nku069218.hh.nku.edu> <20110222184741.GA21681@thebird.nl> Message-ID: <20110222194309.GB5855@nku069218.hh.nku.edu> That's useful to know. I was familiar with FFI but I didn't know it was the preferred approach in Ruby. I'm learning C and hoping to use it where necessary for solving bottle necks. On Tue, Feb 22, 2011 at 07:47:41PM +0100, Pjotr Prins wrote: > On Tue, Feb 22, 2011 at 11:48:21AM -0500, Michael Barton wrote: > > Thank you Naohisa and Francesco for your suggestions. I will try > > experimenting with these two libraries. I had also just read an interesting > > article on using C extensions in Ruby which I thought might be of general > > interest to the mailing list - > > > > http://robots.thoughtbot.com/post/1037240922 > > This discusses using a Ruby C interface. Note: it is not the easiest way. > Especially with existing C libs you may be better off with FFI or SWIG. The > first makes mapping to Ruby easy, the second maps to all languages. For most > Ruby bindings FFI is preferred, also because it does JRuby. > > Binding existing libraries is usually non-trivial. Because C has no GC, and > buffers get passed around as function parameters. > > Pj. From mail at michaelbarton.me.uk Tue Feb 22 19:59:17 2011 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 22 Feb 2011 14:59:17 -0500 Subject: [BioRuby] BioRuby interesting links and documentation. In-Reply-To: <20110222183636.8da2b75f@mail.ingm.it> References: <20110222164821.GA2096@nku069218.hh.nku.edu> <20110222183636.8da2b75f@mail.ingm.it> Message-ID: <20110222195917.GA5949@nku069218.hh.nku.edu> I thought I should reply to Raoul's email with a different topic name. One way could be to share interesting links through some sort of feed? A community blog or twitter? I think the wiki needs some attention in places, e.g. the sample codes page has many headings with "TBD" as the content. The doc rails project seems to have been quite successful for the Rails community. Rather than a wiki it's a static site on github. I think the reason of it's success is that one person is responsible for it (@pratiknaik). On Tue, Feb 22, 2011 at 07:36:36PM +0100, Raoul Bonnal wrote: > Hi Michael, thanks for the post. Why not open a Geek section on the wiki for > this type of links ? _____ > > From: Michael Barton [mailto:mail at michaelbarton.me.uk] To: BioRuby Mailing > List [mailto:bioruby at lists.open-bio.org] Sent: Tue, 22 Feb 2011 17:48:21 > +0100 Subject: Re: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh > C-extension > > Thank you Naohisa and Francesco for your suggestions. I will try > experimenting with these two libraries. I had also just read an interesting > article on using C extensions in Ruby which I thought might be of general > interest to the mailing list - > > http://robots.thoughtbot.com/post/1037240922 > > On Tue, Feb 22, 2011 at 06:11:20PM +0900, Naohisa GOTO wrote: > > Hi, > > > > There was SWlib, an implementation of Smith-Waterman algorithm for Ruby. > > It was written by OKUJI K. Yoshinori in 2001. Since it is very old, some > > modification would be needed for correct working. > > http://bioruby.open-bio.org/contrib/swlib/ > > > > Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > > > On Mon, 21 Feb 2011 12:06:07 -0500 Michael Barton > > wrote: > > > > > Hi, > > > > > > Does anyone know of a ruby library for doing local and global sequence > > > alignment? I'm interested in performing these kind of alignments in > > > ruby but would prefer not to call command line tools such as EMBOSS. > > > I think it could be useful to have a ruby gem which installs > > > a C-extension for allowing for reasonably fast alignment. A cursory > > > look on pubmed turned these links for C libraries. > > > > > > http://www.ncbi.nlm.nih.gov/pubmed/18959793 > > > http://www.ncbi.nlm.nih.gov/books/NBK7151/ > > > > > > Mike > > > > _______________________________________________ BioRuby Project > > - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > From chmille4 at gmail.com Tue Feb 22 20:11:48 2011 From: chmille4 at gmail.com (Chase Miller) Date: Tue, 22 Feb 2011 15:11:48 -0500 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: <20110222194309.GB5855@nku069218.hh.nku.edu> References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> <20110222164821.GA2096@nku069218.hh.nku.edu> <20110222184741.GA21681@thebird.nl> <20110222194309.GB5855@nku069218.hh.nku.edu> Message-ID: My understanding is that a C extension ships the source and compiles on gem installation, whereas FFI requires multiple pre-compiled shared libraries (one for each supported platform) to ship with the gem. Maintaining all those shared libraries sounds like a lot of work. I'm not sure I understand why FFI is preferred; could someone explain it a little more in detail? Chase On Tue, Feb 22, 2011 at 2:43 PM, Michael Barton wrote: > That's useful to know. I was familiar with FFI but I didn't know it was the > preferred approach in Ruby. I'm learning C and hoping to use it where > necessary > for solving bottle necks. > > On Tue, Feb 22, 2011 at 07:47:41PM +0100, Pjotr Prins wrote: > > On Tue, Feb 22, 2011 at 11:48:21AM -0500, Michael Barton wrote: > > > Thank you Naohisa and Francesco for your suggestions. I will try > > > experimenting with these two libraries. I had also just read an > interesting > > > article on using C extensions in Ruby which I thought might be of > general > > > interest to the mailing list - > > > > > > http://robots.thoughtbot.com/post/1037240922 > > > > This discusses using a Ruby C interface. Note: it is not the easiest way. > > Especially with existing C libs you may be better off with FFI or SWIG. > The > > first makes mapping to Ruby easy, the second maps to all languages. For > most > > Ruby bindings FFI is preferred, also because it does JRuby. > > > > Binding existing libraries is usually non-trivial. Because C has no GC, > and > > buffers get passed around as function parameters. > > > > Pj. > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > From pjotr.public14 at thebird.nl Tue Feb 22 22:01:35 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 22 Feb 2011 23:01:35 +0100 Subject: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension In-Reply-To: References: <20110221170607.GA14295@Michael-Bartons-MacBook.local> <20110222091120.B49201CBC3C4@idnmail.gen-info.osaka-u.ac.jp> <20110222164821.GA2096@nku069218.hh.nku.edu> <20110222184741.GA21681@thebird.nl> <20110222194309.GB5855@nku069218.hh.nku.edu> Message-ID: <20110222220135.GC22581@thebird.nl> On Tue, Feb 22, 2011 at 03:11:48PM -0500, Chase Miller wrote: > My understanding is that a C extension ships the source and compiles on gem > installation, whereas FFI requires multiple pre-compiled shared libraries > (one for each supported platform) to ship with the gem. Maintaining all > those shared libraries sounds like a lot of work. > > I'm not sure I understand why FFI is preferred; could someone explain it a > little more in detail? For the C ext you have to learn the Ruby C API. It is C. FFI allows you to define a C mapping in Ruby. You don't even have to write C code. That is the difference. The first option is what Rext does for R, and XS does for Perl. The second is more like generating C bindings, something SWIG does too. Your mileage may vary, but I am glad we can get away from that. Note that when Rext, XS or Ruby C API changes, there may be a lot of work involved (like between Perl 5 and 6). FFI mappings are more portable, also between (future) versions of Ruby, as they *generate* code. Hope that helps. But there is no reason not to dig a little. Nothing replaces experience... Pj. From Yannick.Wurm at unil.ch Wed Feb 23 06:48:21 2011 From: Yannick.Wurm at unil.ch (Yannick Wurm) Date: Wed, 23 Feb 2011 13:48:21 +0700 Subject: [BioRuby] tutorial Message-ID: <031681A4-3307-4F8D-AEF2-7B74668046E3@unil.ch> Hi all, I recently discovered pjotr's updated version of the bioruby tutorial http://thebird.nl/bioruby/Tutorial.rd.html It looks great and seems to be more recent than whats on the bioruby site. Is there any reason the old tutorial is still on the bioruby site? It's a bit confusing. Furthermore, I think newbies are more likely to follow what is on the bioruby site because: - pjotr's tutorials pagerank is lower - the "WARNING: Much of this page works, but we recommend you use the tutorial currently in the distribution as ./doc/Tutorial.rd.html. A recently updated version is here" doesn't stand out at all and so most are unlikely to see it. pjotr: maybe one thing that could make your tutorial easier to read is an index... kind regards, yannick ------------------------- Ant Genomes & Evolution http://yannick.poulet.org skype://yannickwurm From ktym at hgc.jp Wed Feb 23 07:43:47 2011 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 23 Feb 2011 16:43:47 +0900 Subject: [BioRuby] BioRuby GSoC 2011 ideas? References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> Message-ID: <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> Hi all, I just discussed with Rutger about Google Summer of Code (GSoC) 2011. If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. Attached is an announcement from NESCent, which is focused on phloinformatics. I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 http://www.open-bio.org/wiki/Google_Summer_of_Code Some ideas from our side are: for NESCent GSoC, - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) for OBF GSoC, - develop NGS-related plugins - develop a generic framework for workflow management and parallel execution of tasks - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) Regards, Toshiaki Katayama Begin forwarded message: > From: Hilmar Lapp > Date: 2011?2?22? 03:55:52JST > To: PhyloSoC Announcements > Subject: Phyloinformatics Summer of Code 2011: Call for Mentors > Reply-To: phylosoc-announce at googlegroups.com > > Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. > > Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. > > If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). > > If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. > > The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). > > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 > > We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): > > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 > > Dates: > ====== > > Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. > > Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See > http://bit.ly/soc2011-timeline for a full timeline of the whole program. > > Cheers, and we look forward to hearing from you! > > Karen Cranston > Hilmar Lapp > > (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. > > -- > You received this message because you are subscribed to the Google > Groups "Phyloinfomatics Summer of Code Announcements" group. > To unsubscribe from this group, send email to > phylosoc-announce+unsubscribe at googlegroups.com > For more options, visit this group at > http://groups.google.com/group/phylosoc-announce?hl=en From ktym at hgc.jp Wed Feb 23 09:45:36 2011 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 23 Feb 2011 18:45:36 +0900 Subject: [BioRuby] tutorial In-Reply-To: <031681A4-3307-4F8D-AEF2-7B74668046E3@unil.ch> References: <031681A4-3307-4F8D-AEF2-7B74668046E3@unil.ch> Message-ID: Hi Yannick, I agree that we should keep the latest version on the web. I'm not sure which is most recent version, http://thebird.nl/bioruby/Tutorial.rd.html https://github.com/bioruby/bioruby/blob/master/doc/Tutorial.rd but if we convert this Tutrial.rd written in RD format to rdoc format (should be easy), it will be automatically available at, http://bioruby.open-bio.org/rdoc/ however, I don't know there is a best way to synchronize it with http://bioruby.open-bio.org/wiki/Tutorial because Mediawiki format is also a different one from RD and rdoc... Any ideas? Toshiaki On 2011/02/23, at 15:48, Yannick Wurm wrote: > Hi all, > I recently discovered pjotr's updated version of the bioruby tutorial > http://thebird.nl/bioruby/Tutorial.rd.html > > It looks great and seems to be more recent than whats on the bioruby site. Is there any reason the old tutorial is still on the bioruby site? It's a bit confusing. Furthermore, I think newbies are more likely to follow what is on the bioruby site because: > - pjotr's tutorials pagerank is lower > - the "WARNING: Much of this page works, but we recommend you use the tutorial currently in the distribution as ./doc/Tutorial.rd.html. A recently updated version is here" doesn't stand out at all and so most are unlikely to see it. > > pjotr: maybe one thing that could make your tutorial easier to read is an index... > > kind regards, > > yannick > > > ------------------------- > Ant Genomes & Evolution > http://yannick.poulet.org > skype://yannickwurm > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Wed Feb 23 10:51:32 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 23 Feb 2011 11:51:32 +0100 Subject: [BioRuby] tutorial In-Reply-To: References: <031681A4-3307-4F8D-AEF2-7B74668046E3@unil.ch> Message-ID: <20110223105132.GA24543@thebird.nl> On Wed, Feb 23, 2011 at 06:45:36PM +0900, Toshiaki Katayama wrote: > however, I don't know there is a best way to synchronize it with > > http://bioruby.open-bio.org/wiki/Tutorial > > because Mediawiki format is also a different one from RD and rdoc... Any ideas? we should drop the Mediawiki version - despite the nice colours. Pj. From bonnalraoul at ingm.it Wed Feb 23 12:10:30 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 23 Feb 2011 13:10:30 +0100 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> Message-ID: <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Dear All, I remind you about the irc meeting for live discussion, I think the main topic can be GSoC 2011 I'd like to have some update about Semantic Web its reliability and if we (bioruby) are going to use it. Where? I'm available for mentoring on OBF GSoC projects. On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: > Hi all, > > I just discussed with Rutger about Google Summer of Code (GSoC) 2011. > If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. > > Attached is an announcement from NESCent, which is focused on phloinformatics. > I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). > > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 > http://www.open-bio.org/wiki/Google_Summer_of_Code > > Some ideas from our side are: > > for NESCent GSoC, > - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) > > for OBF GSoC, > - develop NGS-related plugins > - develop a generic framework for workflow management and parallel execution of tasks > - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) > > Regards, > Toshiaki Katayama > > Begin forwarded message: > >> From: Hilmar Lapp >> Date: 2011?2?22? 03:55:52JST >> To: PhyloSoC Announcements >> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors >> Reply-To: phylosoc-announce at googlegroups.com >> >> Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. >> >> Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. >> >> If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). >> >> If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. >> >> The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). >> >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >> >> We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): >> >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 >> >> Dates: >> ====== >> >> Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. >> >> Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See >> http://bit.ly/soc2011-timeline for a full timeline of the whole program. >> >> Cheers, and we look forward to hearing from you! >> >> Karen Cranston >> Hilmar Lapp >> >> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. >> >> -- >> You received this message because you are subscribed to the Google >> Groups "Phyloinfomatics Summer of Code Announcements" group. >> To unsubscribe from this group, send email to >> phylosoc-announce+unsubscribe at googlegroups.com >> For more options, visit this group at >> http://groups.google.com/group/phylosoc-announce?hl=en > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra From anurag08priyam at gmail.com Wed Feb 23 12:55:21 2011 From: anurag08priyam at gmail.com (Anurag Priyam) Date: Wed, 23 Feb 2011 18:25:21 +0530 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> Message-ID: > for OBF GSoC, > - develop NGS-related plugins > - develop a generic framework for workflow management and parallel execution of tasks > - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) Rutger had earlier informed me that he has decided to refactor my last years's GSoC work into two separate plugins - bio-nexml, and bio-rdf. While Rutger has already started to work on bio-nexml, bio-rdf still needs to take shape (which would also be a dependency for bio-nexml). Since it is very likely that the "Semantic Web Plugins" idea would relate closely to bio-rdf, I can help there. I intend to participate again in GSoC this year as a student, so I could either undertake it as a project, or, (co-)mentor *non-officially*. -- Anurag Priyam http://about.me/yeban/ From francesco.strozzi at gmail.com Wed Feb 23 13:20:35 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Wed, 23 Feb 2011 14:20:35 +0100 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Message-ID: I'm available too for mentoring or co-mentoring with Raoul, particularly on NGS plugins. In these days I'm working on the main NGS plugin and I think one interesting topic will be to develop a workflow plugin to handle multiple (and parallel) NGS tasks and also other type of bio-analyses, as discussed during the last IRC call. OBF GSoC could be a good opportunity to develop such a plugin. Cheers Francesco On Wed, Feb 23, 2011 at 13:10, Raoul Bonnal wrote: > Dear All, > I remind you about the irc meeting for live discussion, I think the main > topic can be GSoC 2011 > > I'd like to have some update about Semantic Web its reliability and if we > (bioruby) are going to use it. Where? > > I'm available for mentoring on OBF GSoC projects. > > On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: > > > Hi all, > > > > I just discussed with Rutger about Google Summer of Code (GSoC) 2011. > > If you are interested in to mentor/participate GSoC this year, please put > your ideas on this list. > > > > Attached is an announcement from NESCent, which is focused on > phloinformatics. > > I heard that Open Bio Foundation (OBF) is also considering to organize > GSoC again (not confirmed, though). > > > > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 > > http://www.open-bio.org/wiki/Google_Summer_of_Code > > > > Some ideas from our side are: > > > > for NESCent GSoC, > > - compile phyloinfo plugins for BioRuby (based on NEXML > https://github.com/rvosa/bio-nexml, forester > http://code.google.com/p/forester/ etc.) to make analysis pipeline > available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully > ;) > > > > for OBF GSoC, > > - develop NGS-related plugins > > - develop a generic framework for workflow management and parallel > execution of tasks > > - develop plugins for Semantic Web (RDF utilities, SPARQL query > interface, handling ontologies etc.) > > > > Regards, > > Toshiaki Katayama > > > > Begin forwarded message: > > > >> From: Hilmar Lapp > >> Date: 2011?2?22? 03:55:52JST > >> To: PhyloSoC Announcements > >> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors > >> Reply-To: phylosoc-announce at googlegroups.com > >> > >> Over the next 3 weeks we will be pulling together NESCent's application > to the 2011 Google Summer of Code as a mentoring organization. This is a > call for all prospective mentors, primary and secondary, to step forward. > >> > >> Participating as an organization is competitive. Over the last years the > acceptance rate for organizations has been around 30-35%. The most important > component of organization applications is the Ideas page, and specifically > the quality and suitability of the project ideas. These project ideas are > contributed by you, our mentors. In the past we have had a strong, diverse > and well-documented portfolio of ideas with different degrees of difficulty, > from different participating open-source projects, using different > programming languages. > >> > >> If you can fancy yourself serving as a mentor, or helping someone else > mentoring a student as a secondary mentor, or would like to help out in > other capacities, please contact us as soon as you can at > phylosoc-admin at nescent.org. If you have not been a mentor with us in > previous years, we'll send you guidance on what doing so involves, and how > you can contribute to our participation. We will also add everyone who is > interested in serving to our (private) mentors mailing list (at least those > who aren't already). > >> > >> If you are new to Summer of Code and wonder what it takes or what it is > like to be a mentor for us, don't hesitate to ask questions or to contact > previous mentors (see URLs below for projects that got selected). Being a > mentor does require time (see http://bit.ly/soc2011-mentortime), but our > past mentors have pretty much unanimously found it a fun and rewarding > experience. That's aside from the code a student could contribute to your > project, and, possibly most important of all in the long run, the chance to > gain a new developer. > >> > >> The initial skeleton of our 2011 Ideas page is now up here and ready for > adding project ideas and mentors(*). > >> > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 > >> > >> We will send further guidance on drafting project ideas, but for now you > can see examples of the format and scope of project ideas on the Ideas pages > from previous years (click on "Ideas"): > >> > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 > >> > http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 > >> > >> Dates: > >> ====== > >> > >> Submission of organization applications starts Feb 28 and closes on > March 11. For project ideas to contribute to the strength of our application > they must be in reasonable shape by the morning of March 11. *If* we are > accepted, ideas can be refined (or added) between March 18-27. > >> > >> Students apply March 28-April 8, and selected students are announced > April 25. The coding period runs from May 23 to August 22. See > >> http://bit.ly/soc2011-timeline for a full timeline of the whole > program. > >> > >> Cheers, and we look forward to hearing from you! > >> > >> Karen Cranston > >> Hilmar Lapp > >> > >> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon > wiki) requires you to login. We had to disable local account creation due to > spam getting out of control. The wiki is still open, though - just login > with your OpenID. If you don't have an OpenID, the "Login with OpenID" page > has information on you can easily get one, and if you have a Google account, > you're all set to go. > >> > >> -- > >> You received this message because you are subscribed to the Google > >> Groups "Phyloinfomatics Summer of Code Announcements" group. > >> To unsubscribe from this group, send email to > >> phylosoc-announce+unsubscribe at googlegroups.com > >> For more options, visit this group at > >> http://groups.google.com/group/phylosoc-announce?hl=en > > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > -- > Ra > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From cjfields at illinois.edu Wed Feb 23 14:42:09 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 23 Feb 2011 08:42:09 -0600 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Message-ID: It's probably also a good idea to consolidate BioRuby ideas on a specific GSoC 2011 page. Not sure if Rob Buels has set that up yet, will check into it. chris On Feb 23, 2011, at 6:10 AM, Raoul Bonnal wrote: > Dear All, > I remind you about the irc meeting for live discussion, I think the main topic can be GSoC 2011 > > I'd like to have some update about Semantic Web its reliability and if we (bioruby) are going to use it. Where? > > I'm available for mentoring on OBF GSoC projects. > > On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: > >> Hi all, >> >> I just discussed with Rutger about Google Summer of Code (GSoC) 2011. >> If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. >> >> Attached is an announcement from NESCent, which is focused on phloinformatics. >> I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). >> >> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >> http://www.open-bio.org/wiki/Google_Summer_of_Code >> >> Some ideas from our side are: >> >> for NESCent GSoC, >> - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) >> >> for OBF GSoC, >> - develop NGS-related plugins >> - develop a generic framework for workflow management and parallel execution of tasks >> - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) >> >> Regards, >> Toshiaki Katayama >> >> Begin forwarded message: >> >>> From: Hilmar Lapp >>> Date: 2011?2?22? 03:55:52JST >>> To: PhyloSoC Announcements >>> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors >>> Reply-To: phylosoc-announce at googlegroups.com >>> >>> Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. >>> >>> Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. >>> >>> If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). >>> >>> If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. >>> >>> The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). >>> >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>> >>> We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): >>> >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 >>> >>> Dates: >>> ====== >>> >>> Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. >>> >>> Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See >>> http://bit.ly/soc2011-timeline for a full timeline of the whole program. >>> >>> Cheers, and we look forward to hearing from you! >>> >>> Karen Cranston >>> Hilmar Lapp >>> >>> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "Phyloinfomatics Summer of Code Announcements" group. >>> To unsubscribe from this group, send email to >>> phylosoc-announce+unsubscribe at googlegroups.com >>> For more options, visit this group at >>> http://groups.google.com/group/phylosoc-announce?hl=en >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > -- > Ra > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnalraoul at ingm.it Wed Feb 23 15:11:02 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 23 Feb 2011 16:11:02 +0100 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Message-ID: Good point Chris. Do you want to join us, tomorrow ? On 23/feb/2011, at 15.42, Chris Fields wrote: > It's probably also a good idea to consolidate BioRuby ideas on a specific GSoC 2011 page. Not sure if Rob Buels has set that up yet, will check into it. > > chris > > On Feb 23, 2011, at 6:10 AM, Raoul Bonnal wrote: > >> Dear All, >> I remind you about the irc meeting for live discussion, I think the main topic can be GSoC 2011 >> >> I'd like to have some update about Semantic Web its reliability and if we (bioruby) are going to use it. Where? >> >> I'm available for mentoring on OBF GSoC projects. >> >> On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: >> >>> Hi all, >>> >>> I just discussed with Rutger about Google Summer of Code (GSoC) 2011. >>> If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. >>> >>> Attached is an announcement from NESCent, which is focused on phloinformatics. >>> I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). >>> >>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>> http://www.open-bio.org/wiki/Google_Summer_of_Code >>> >>> Some ideas from our side are: >>> >>> for NESCent GSoC, >>> - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) >>> >>> for OBF GSoC, >>> - develop NGS-related plugins >>> - develop a generic framework for workflow management and parallel execution of tasks >>> - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) >>> >>> Regards, >>> Toshiaki Katayama >>> >>> Begin forwarded message: >>> >>>> From: Hilmar Lapp >>>> Date: 2011?2?22? 03:55:52JST >>>> To: PhyloSoC Announcements >>>> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors >>>> Reply-To: phylosoc-announce at googlegroups.com >>>> >>>> Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. >>>> >>>> Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. >>>> >>>> If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). >>>> >>>> If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. >>>> >>>> The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). >>>> >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>>> >>>> We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): >>>> >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 >>>> >>>> Dates: >>>> ====== >>>> >>>> Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. >>>> >>>> Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See >>>> http://bit.ly/soc2011-timeline for a full timeline of the whole program. >>>> >>>> Cheers, and we look forward to hearing from you! >>>> >>>> Karen Cranston >>>> Hilmar Lapp >>>> >>>> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "Phyloinfomatics Summer of Code Announcements" group. >>>> To unsubscribe from this group, send email to >>>> phylosoc-announce+unsubscribe at googlegroups.com >>>> For more options, visit this group at >>>> http://groups.google.com/group/phylosoc-announce?hl=en >>> >>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> -- >> Ra >> >> >> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > -- Ra From cjfields at illinois.edu Wed Feb 23 15:59:52 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 23 Feb 2011 09:59:52 -0600 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> Message-ID: <7C26CA61-02C4-4424-B074-E37E6B88B565@illinois.edu> Let me know the IRC server, channel, and time, and I'll check in. Not sure how the time will sync but I can always try. chris On Feb 23, 2011, at 9:11 AM, Raoul Bonnal wrote: > Good point Chris. > Do you want to join us, tomorrow ? > On 23/feb/2011, at 15.42, Chris Fields wrote: > >> It's probably also a good idea to consolidate BioRuby ideas on a specific GSoC 2011 page. Not sure if Rob Buels has set that up yet, will check into it. >> >> chris >> >> On Feb 23, 2011, at 6:10 AM, Raoul Bonnal wrote: >> >>> Dear All, >>> I remind you about the irc meeting for live discussion, I think the main topic can be GSoC 2011 >>> >>> I'd like to have some update about Semantic Web its reliability and if we (bioruby) are going to use it. Where? >>> >>> I'm available for mentoring on OBF GSoC projects. >>> >>> On 23/feb/2011, at 08.43, Toshiaki Katayama wrote: >>> >>>> Hi all, >>>> >>>> I just discussed with Rutger about Google Summer of Code (GSoC) 2011. >>>> If you are interested in to mentor/participate GSoC this year, please put your ideas on this list. >>>> >>>> Attached is an announcement from NESCent, which is focused on phloinformatics. >>>> I heard that Open Bio Foundation (OBF) is also considering to organize GSoC again (not confirmed, though). >>>> >>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>>> http://www.open-bio.org/wiki/Google_Summer_of_Code >>>> >>>> Some ideas from our side are: >>>> >>>> for NESCent GSoC, >>>> - compile phyloinfo plugins for BioRuby (based on NEXML https://github.com/rvosa/bio-nexml, forester http://code.google.com/p/forester/ etc.) to make analysis pipeline available (relevant to Bio::Phylo in Perl) - with a nice tutorial, hopefully ;) >>>> >>>> for OBF GSoC, >>>> - develop NGS-related plugins >>>> - develop a generic framework for workflow management and parallel execution of tasks >>>> - develop plugins for Semantic Web (RDF utilities, SPARQL query interface, handling ontologies etc.) >>>> >>>> Regards, >>>> Toshiaki Katayama >>>> >>>> Begin forwarded message: >>>> >>>>> From: Hilmar Lapp >>>>> Date: 2011?2?22? 03:55:52JST >>>>> To: PhyloSoC Announcements >>>>> Subject: Phyloinformatics Summer of Code 2011: Call for Mentors >>>>> Reply-To: phylosoc-announce at googlegroups.com >>>>> >>>>> Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. >>>>> >>>>> Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. >>>>> >>>>> If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin at nescent.org. If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). >>>>> >>>>> If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime), but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. >>>>> >>>>> The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). >>>>> >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 >>>>> >>>>> We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): >>>>> >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 >>>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 >>>>> >>>>> Dates: >>>>> ====== >>>>> >>>>> Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. >>>>> >>>>> Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See >>>>> http://bit.ly/soc2011-timeline for a full timeline of the whole program. >>>>> >>>>> Cheers, and we look forward to hearing from you! >>>>> >>>>> Karen Cranston >>>>> Hilmar Lapp >>>>> >>>>> (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go. >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "Phyloinfomatics Summer of Code Announcements" group. >>>>> To unsubscribe from this group, send email to >>>>> phylosoc-announce+unsubscribe at googlegroups.com >>>>> For more options, visit this group at >>>>> http://groups.google.com/group/phylosoc-announce?hl=en >>>> >>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >>> -- >>> Ra >>> >>> >>> >>> >>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> > > -- > Ra > > > > From anurag08priyam at gmail.com Wed Feb 23 16:14:25 2011 From: anurag08priyam at gmail.com (Anurag Priyam) Date: Wed, 23 Feb 2011 21:44:25 +0530 Subject: [BioRuby] BioRuby GSoC 2011 ideas? In-Reply-To: <7C26CA61-02C4-4424-B074-E37E6B88B565@illinois.edu> References: <28297803-062D-4C40-A6F6-999A71A2D176@nescent.org> <9C15E792-54F7-44F7-986B-9CD413E03BE1@hgc.jp> <116E7FA5-1886-4DA0-93B1-AAB83EE34DB0@ingm.it> <7C26CA61-02C4-4424-B074-E37E6B88B565@illinois.edu> Message-ID: > Let me know the IRC server, channel, and time, and I'll check in. ?Not sure how the time will sync but I can always try. #bioruby on Freenode See timings at: http://bioruby.open-bio.org/wiki/BioRuby_IRC_conference -- Anurag Priyam http://about.me/yeban/ From cmzmasek at yahoo.com Thu Feb 24 19:00:08 2011 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Thu, 24 Feb 2011 11:00:08 -0800 (PST) Subject: [BioRuby] BioRuby multiple sequence alignment and phylogenetics tutorial Message-ID: <656365.18864.qm@web38406.mail.mud.yahoo.com> Hi, all: I (finally) started to work on the promised multiple sequence alignment and phylogenetics tutorial. You can see the "development" version (not much more than a scaffold at this point) here: http://code.google.com/p/forester/wiki/PhyloBioRuby (Obviously this needs to be moved once it approaches completeness.) Any comments? Please note: 1. In order to allow BioRuby to run at least a very simple phylogenetic inference 'pipeline' (unaligned sequences to phylogenetic tree), I am thinking about writing wrappers for RAxML and FastME and possibly some programs from the PHYLIP package. 2. I still need to test (and clean up) Sarah Rayburn's GSoC code ('SDI') so that it can be considered for inclusion into the main BioRuby distribution. Christian Zmasek PS. We discussed this a little on the BioRuby irc-conference 24. Feb. 2011. From bonnalraoul at ingm.it Fri Feb 25 08:52:59 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 25 Feb 2011 09:52:59 +0100 Subject: [BioRuby] BioRuby+BioGem@Ruby Social Club in Milan Message-ID: Dear All, yesterday I talked about BioRuby and BioGem projects during a Ruby Meeting in Milan. Sorry the presentation is in Italian, I'll translate it in english asap if you are interested. It was a small meeting with few people but they were very interested about our projects. I think because we are facing problems that are not so common, basically the business is more "standard" than expected :-). Many of them believe that bioinformatics is just crunching data. Others known our friends BioPerl and BioPython and nothing about BioRuby. Why ? One or two guys that know BioPython were exited about BioRuby; the answer is simple, at university they learned perl or python, ruby is just relegated to business work aka Rails. What that means for me ? Perl is an institution :-) ,Python's guys did a great job in spreading their project. How can we change the world :-) ? Talking! and in June ( I can't remember the date, around 12) there will be the Ruby Day -Italy- at University of Milano Bicocca and I'm going to help as much as possible in this event. Actually I hope to take part in the organization, everything needs to be planned, talks, tutorials.... etc I'm very surprised for a so strong and vivid interest. The meeting schedule: - Giordano Scalzo. MongoMapper , a wrapper for MongoDB - Raoul Bonnal. BioRuby and BioGem, how to create gems that can be reused from script and rails application aka engines BioGem - Andrea Reginato. Testing ed RSpec best practices. NOTE: please contribute to the document is free and open !!! -Elia Schito:TimeTap helps you track the time you spend coding on each project while in TextMate https://github.com/elia/timetap Just few link that can be of interest for Bio* projetcs, I know that Peter and Chris are reading: >>> CeBIT di Hannover nell'ambito dell'"Open >>> Source Park" >>> >>> http://www.cebit.de/exhibitor/vemar?directLink=Y854924 >>> http://www.open-source-park.com/ > www.nosqlday.it sold out (just for note) MongoUK - 21 March http://www.10gen.com/conferences/mongouk2011 Mongo France - 23 March http://lacantine.org/events/mongo-france-2011 http://www.10gen.com/conferences/mongofr2011 Mongo Berlin - 25 March http://www.10gen.com/conferences/mongoberlin2011 It would be very useful to have a shared calendar where putting this kind of events. Do we agree to use google calendar or do you have a better solution ? Ciao! -- Ra From rob.syme at gmail.com Sat Feb 26 21:36:52 2011 From: rob.syme at gmail.com (Rob Syme) Date: Sun, 27 Feb 2011 05:36:52 +0800 Subject: [BioRuby] Move your ass at this site! Message-ID: Multiple orgasms with your lover!!!.. http://ulf.lass-trocknen.de/links.php?facgoogle=366 From bonnalraoul at ingm.it Mon Feb 28 16:07:54 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Mon, 28 Feb 2011 17:07:54 +0100 Subject: [BioRuby] BestPracties for wrappers Message-ID: Dear Goto-san, if I would write a new wrapper for a new program, using Bio::Command libs, which are the best practies ? looking into the other wrappers the code is not always, let' say "standard" Could you give me some hints ? -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From cmzmasek at yahoo.com Mon Feb 28 19:14:15 2011 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Mon, 28 Feb 2011 11:14:15 -0800 (PST) Subject: [BioRuby] BestPracties for wrappers In-Reply-To: References: Message-ID: <508088.59531.qm@web38402.mail.mud.yahoo.com> Good point! I also would be interested in that! Christian ----- Original Message ---- > From: Raoul Bonnal > To: BioRuby ML > Sent: Mon, February 28, 2011 8:07:54 AM > Subject: [BioRuby] BestPracties for wrappers > > Dear Goto-san, > if I would write a new wrapper for a new program, using Bio::Command libs, >which are the best practies ? > looking into the other wrappers the code is not always, let' say "standard" > Could you give me some hints ? > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby >