From marian.povolny at gmail.com Wed Aug 1 08:46:44 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Wed, 1 Aug 2012 14:46:44 +0200 Subject: [BioRuby] GSoC weekly status report No.9 Message-ID: http://blog.mpthecoder.com/post/28481171942/gsoc-weekly-status-report-no-9 The trip to Lodi was very fruitful. It was great to meet both my mentor and other community members. Based on the input received at the codefest, I created a new plan for the second part of the summer: https://github.com/mamarjan/gff3-pltools/wiki/Part2 Since then I have done the following: - improved validation speed, - added GTF support for input and output, - table output with an option to select which fields and attributes should be in the table, - tools for conversion to GTF and JSON, - JSON output support, which needs some more polish. -- Marjan From pjotr.public14 at thebird.nl Sat Aug 4 07:07:42 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 4 Aug 2012 13:07:42 +0200 Subject: [BioRuby] BioRuby passes tests (kinda)! Message-ID: <20120804110742.GA7701@thebird.nl> Anyone noticed that BioRuby has gone green on http://biogems.info/? Not all tests pass, but Travis has a new function for telling it what versions of Ruby are *allowed* to fail. Heh. Be good when JRuby1.9 starts passing. Pj. From p.j.a.cock at googlemail.com Sat Aug 4 09:29:59 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 4 Aug 2012 14:29:59 +0100 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: <20120804110742.GA7701@thebird.nl> References: <20120804110742.GA7701@thebird.nl> Message-ID: On Sat, Aug 4, 2012 at 12:07 PM, Pjotr Prins wrote: > Anyone noticed that BioRuby has gone green on http://biogems.info/? > No - but I did notice it on the recent blog post: http://news.open-bio.org/news/2012/07/travis-ci-for-testing/ > Not all tests pass, but Travis has a new function for telling it what > versions of Ruby are *allowed* to fail. > > Heh. Good plan. > Be good when JRuby1.9 starts passing. > Do you know what the general problem is? Peter From ngoto at gen-info.osaka-u.ac.jp Sat Aug 4 11:48:54 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Sun, 05 Aug 2012 00:48:54 +0900 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: References: <20120804110742.GA7701@thebird.nl> Message-ID: <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> Hi, > On Sat, Aug 4, 2012 at 12:07 PM, Pjotr Prins wrote: > > Anyone noticed that BioRuby has gone green on http://biogems.info/? I've changed .travis.yml yesterday. https://github.com/bioruby/bioruby/commit/9a2fe67c247cdc7c9ddc9f8b8de771515ba76ac1 After the change, the status has been shown as "green". Keeping "green" status is important for using the automatic testing of pull requests by Travis-CI. On Sat, 4 Aug 2012 14:29:59 +0100, Peter Cock wrote: > No - but I did notice it on the recent blog post: > http://news.open-bio.org/news/2012/07/travis-ci-for-testing/ Thanks. > > Be good when JRuby1.9 starts passing. > > Do you know what the general problem is? I think some of them might be due to bugs in JRuby, but further investigation is needed. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From ngoto at gen-info.osaka-u.ac.jp Sat Aug 4 12:37:13 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Sun, 05 Aug 2012 01:37:13 +0900 Subject: [BioRuby] BioRuby 1.4.3 will soon be released Message-ID: <20120805013713.18B0.EEF6E030@gen-info.osaka-u.ac.jp> Hi all, I'd like to release a new version of BioRuby, BioRuby 1.4.3. This is minor maintainance release, mostly consisted of bug fixes. The new version also improves of portability running on Jruby and Rubinius. In the new version, little incompatible changes are made due to the side effects of some bug fixes. See RELEASE_NOTES.rdoc for more information (work in progress) https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc If you have any comments (or objections), please respond soon. I'd like to relase it in hurry, because almost 1 year has passed since the last release of 1.4.2. Note that the aim of the new version is bug fix. After the release, some new features may be added and some incompatible drastic changes may be made. Thanks, -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From cswh at umich.edu Sat Aug 4 12:42:21 2012 From: cswh at umich.edu (Clayton Wheeler) Date: Sat, 4 Aug 2012 12:42:21 -0400 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> References: <20120804110742.GA7701@thebird.nl> <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Sat, Aug 4, 2012 at 11:48 AM, Naohisa Goto wrote: > Hi, > >> On Sat, Aug 4, 2012 at 12:07 PM, Pjotr Prins wrote: >> > Anyone noticed that BioRuby has gone green on http://biogems.info/? > > I've changed .travis.yml yesterday. > https://github.com/bioruby/bioruby/commit/9a2fe67c247cdc7c9ddc9f8b8de771515ba76ac1 > After the change, the status has been shown as "green". > > Keeping "green" status is important for using the automatic testing of > pull requests by Travis-CI. > > On Sat, 4 Aug 2012 14:29:59 +0100, Peter Cock > wrote: >> No - but I did notice it on the recent blog post: >> http://news.open-bio.org/news/2012/07/travis-ci-for-testing/ > > Thanks. > >> > Be good when JRuby1.9 starts passing. >> >> Do you know what the general problem is? > > I think some of them might be due to bugs in JRuby, but > further investigation is needed. One of the JRuby bugs I filed on the basis of our test failures has been fixed, and that fix will be out in the next 1.7 preview release if it's not in the current one. Another (an autoload bug causing quite a few failures) has a fix that hasn't been integrated yet; I'll see if I can get that in for 1.7.0.preview2. Also, I've seen quite a few failures involving PhyloXML (particularly on JRuby); now that I've repackaged that as a bio-phyloxml gem (https://github.com/csw/bioruby-phyloxml, which is passing its tests on Travis-CI), we could think about removing it from the main BioRuby repository. -- Clayton Wheeler cswh at umich.edu From ngoto at gen-info.osaka-u.ac.jp Sun Aug 5 03:17:38 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Sun, 5 Aug 2012 16:17:38 +0900 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: References: <20120804110742.GA7701@thebird.nl> <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <201208050717.q757HdJR010728@portal.open-bio.org> On Sat, 4 Aug 2012 12:42:21 -0400 Clayton Wheeler wrote: > Also, I've seen quite a few failures involving PhyloXML (particularly > on JRuby); now that I've repackaged that as a bio-phyloxml gem > (https://github.com/csw/bioruby-phyloxml, which is passing its tests > on Travis-CI), we could think about removing it from the main BioRuby > repository. I'm againt to remove PhyloXML parts from the main repository only because the tests show many failures on JRuby. It runs without errors and errors on MRI (1.8.7, 1.9.2, 1.9.3) and Rubinius (1.8 mode). Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From cswh at umich.edu Sun Aug 5 19:24:58 2012 From: cswh at umich.edu (Clayton Wheeler) Date: Sun, 5 Aug 2012 19:24:58 -0400 Subject: [BioRuby] bio-maf update: BGZF and testing Message-ID: Hi all, I've posted an update on my most recent work on bio-maf. Highlights include BGZF compression support, a new maf_extract command-line tool for random access, and my discoveries from testing on the full UCSC multiz46way dataset. http://csw.github.com/bioruby-maf/blog/2012/08/05/bgzf_and_testing/ -- Clayton Wheeler cswh at umich.edu From lomereiter at gmail.com Mon Aug 6 06:33:54 2012 From: lomereiter at gmail.com (Artem Tarasov) Date: Mon, 6 Aug 2012 14:33:54 +0400 Subject: [BioRuby] [ruby code quality] Code Climate Message-ID: Hi all, Today I've stumbled upon github_api gem, and there is a badge next to Travis CI one, linking to Code Climate. As it turned out, Code Climate is a static analysis tool for Ruby code which helps to find various code smells. Less than a month ago they made their service free for github users: http://blog.codeclimate.com/blog/2012/07/10/code-climate-is-free-for-open-source/ As far as I understand, code analysis is done weekly (not on each push, like Travis CI), and notification is sent via email. IMHO everyone should go and use it :) From lomereiter at gmail.com Tue Aug 7 01:14:02 2012 From: lomereiter at gmail.com (Artem Tarasov) Date: Tue, 7 Aug 2012 05:14:02 +0000 Subject: [BioRuby] [GSoC] weekly report #11 Message-ID: Hello all, here's my latest report about work on sambamba: http://lomereiter.wordpress.com/2012/08/06/gsoc-weekly-report-11/ * simple internal DSL for filtering was introduced in bindings (description: https://github.com/lomereiter/bioruby-sambamba/blob/master/features/filtering.feature ) * BAM output support was added to filtering tool (sambamba view) * man pages for all tools were created * a script was written for building Debian packages and uploading them to Github * Debian packages for v0.2.1 are added to Github downloads (for both i386 and amd64) Now the goal is to make those tools accessible at Galaxy Tool Shed, and also this week I plan to optimize memory usage -- buffer sizes are quite large now, and the task is to find out how much they can be reduced without significant impact on performance. From pjotr.public14 at thebird.nl Tue Aug 7 06:42:24 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 7 Aug 2012 12:42:24 +0200 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: <201208050717.q757HdJR010728@portal.open-bio.org> References: <20120804110742.GA7701@thebird.nl> <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> <201208050717.q757HdJR010728@portal.open-bio.org> Message-ID: <20120807104224.GA25493@thebird.nl> On Sun, Aug 05, 2012 at 04:17:38PM +0900, Naohisa GOTO wrote: > On Sat, 4 Aug 2012 12:42:21 -0400 > Clayton Wheeler wrote: > > > Also, I've seen quite a few failures involving PhyloXML (particularly > > on JRuby); now that I've repackaged that as a bio-phyloxml gem > > (https://github.com/csw/bioruby-phyloxml, which is passing its tests > > on Travis-CI), we could think about removing it from the main BioRuby > > repository. > > I'm againt to remove PhyloXML parts from the main repository > only because the tests show many failures on JRuby. It runs > without errors and errors on MRI (1.8.7, 1.9.2, 1.9.3) and > Rubinius (1.8 mode). I agree the failing tests are not a reason for removing phyloxml. One thing we should discuss, however, is removing code from BioRuby when functional replacements exist, as it the case with bioruby-phyloxml. It makes little sense to maintain two source trees (even if they are phylo trees). Also, we may strip out parts of BioRuby which are not used anymore, or not-so-core, and push those out into biogems. That way BioRuby becomes 'lighter', easier to maintain and modify. That discussion we will have in Japan at the Biohackaton. Perhaps on the way to BioRuby 2.0, and even 3.0. Personally I am also developing ideas on what BioRuby should be, and what it should do. Currently I see the main use of the Bio* projects as being parsers and outputters of the pletora of Bioinformatics of data formats. Maybe we should stick to that, support any known input type, and generalized output, where output should at least support tabular output, JSON, XML, and RDF. All other stuff should go into biogems. Pj. From francesco.strozzi at gmail.com Tue Aug 7 09:23:53 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Tue, 7 Aug 2012 15:23:53 +0200 Subject: [BioRuby] Bio-Incanter Message-ID: Hi guys, after having played for a while with Clojure and Incanter (http://www.incanter.org/), we thought it was nice to have a Ruby gem to access such a great library, so I would like to point out a new BioGem called Bio-Incanter https://github.com/cerbero/bioruby-incanter . This gem was started by Matteo Picciolini, a bioinformatician working in my group here in Italy. He's at the first contribution in the BioRuby world, so be nice! The gem it's a JRuby wrapper around the Incanter library to provide nice and powerful functions to create plots and graphs for numerical and statistical analyses. Look at the specs to see what methods are available, but basically all the common plotting functions are covered, including image export in PNG, JPG or PDF format. There is also a "view" method that can let you open the graphs in real time and see what you are plotting, a nice function for scripts or IRB sessions. Even if you don't know Clojure that's not a problem, the gem takes care of everything and includes a ready to use Jar with both Clojure and Incanter. I think this kind of gems show how JRuby can facilitate the life of a bioinformatician, using existing solutions that just work and providing the best out of (Bio)Ruby and the JVM. -- Francesco From marian.povolny at gmail.com Tue Aug 7 09:36:04 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Tue, 7 Aug 2012 15:36:04 +0200 Subject: [BioRuby] GSoC weekly status report No.10 Message-ID: http://blog.mpthecoder.com/post/28907136767/gsoc-weekly-status-report-no-10 The 0.3 release is available on the website: http://mamarjan.github.com/gff3-pltools/ In addition to what was described in the last weekly report, a GFF3 sorting tool has been added, grouping records which belong to the same feature, and Ruby bindings have been updated to support GTF and new options in gff3-ffetch. -- Marjan From donttrustben at gmail.com Tue Aug 7 20:20:38 2012 From: donttrustben at gmail.com (Ben Woodcroft) Date: Wed, 8 Aug 2012 10:20:38 +1000 Subject: [BioRuby] Bio-Incanter In-Reply-To: References: Message-ID: Hi guys, sounds cool on the face of it to me, thanks. Congrats to Matteo. Annoyingly http://data-sorcery.org is being difficult to access for me. Any chance you could add a simple example(s) to the README or wiki? On 7 August 2012 23:23, Francesco Strozzi wrote: > Hi guys, > after having played for a while with Clojure and Incanter > (http://www.incanter.org/), we thought it was nice to have a Ruby gem > to access such a great library, so I would like to point out a new > BioGem called Bio-Incanter https://github.com/cerbero/bioruby-incanter > . > This gem was started by Matteo Picciolini, a bioinformatician working > in my group here in Italy. He's at the first contribution in the > BioRuby world, so be nice! > > The gem it's a JRuby wrapper around the Incanter library to provide > nice and powerful functions to create plots and graphs for numerical > and statistical analyses. > Look at the specs to see what methods are available, but basically all > the common plotting functions are covered, including image export in > PNG, JPG or PDF format. There is also a "view" method that can let you > open the graphs in real time and see what you are plotting, a nice > function for scripts or IRB sessions. > Even if you don't know Clojure that's not a problem, the gem takes > care of everything and includes a ready to use Jar with both Clojure > and Incanter. > > I think this kind of gems show how JRuby can facilitate the life of a > bioinformatician, using existing solutions that just work and > providing the best out of (Bio)Ruby and the JVM. > > -- > > Francesco > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- -- Ben Woodcroft http://ecogenomic.org/users/ben-woodcroft From donttrustben at gmail.com Wed Aug 8 03:23:21 2012 From: donttrustben at gmail.com (Ben Woodcroft) Date: Wed, 8 Aug 2012 17:23:21 +1000 Subject: [BioRuby] New biogems for ipcress, krona and small kmer counting Message-ID: More adverts.. bio-ipcress is a programmatic interface to exonerate's ipcress, an in-silico PCR system. https://github.com/wwood/bioruby-ipcress bio-krona is a programmatic interface to Krona, a HTML visualisation tool for hierarchical data. https://github.com/wwood/bioruby-krona bio-kmer_counter is a pure ruby gem for counting small kmers (e.g. 4mers) within sequences, for fingerprinting purposes e.g. the binning of metagenomic data. https://github.com/wwood/bioruby-kmer_counter Enjoy, ben -- -- Ben Woodcroft http://ecogenomic.org/users/ben-woodcroft From matteo.picciolini at gmail.com Wed Aug 8 06:00:44 2012 From: matteo.picciolini at gmail.com (Matteo Picciolini) Date: Wed, 8 Aug 2012 12:00:44 +0200 Subject: [BioRuby] Bio-Incanter In-Reply-To: References: Message-ID: Hi guys . I write a simple wiki with two examples to use bio-incanter . https://github.com/cerbero/bioruby-incanter/wiki Enjoy ! 2012/8/8 Ben Woodcroft > Hi guys, sounds cool on the face of it to me, thanks. Congrats to Matteo. > > Annoyingly http://data-sorcery.org is being difficult to access for me. > Any > chance you could add a simple example(s) to the README or wiki? > > On 7 August 2012 23:23, Francesco Strozzi >wrote: > > > Hi guys, > > after having played for a while with Clojure and Incanter > > (http://www.incanter.org/), we thought it was nice to have a Ruby gem > > to access such a great library, so I would like to point out a new > > BioGem called Bio-Incanter https://github.com/cerbero/bioruby-incanter > > . > > This gem was started by Matteo Picciolini, a bioinformatician working > > in my group here in Italy. He's at the first contribution in the > > BioRuby world, so be nice! > > > > The gem it's a JRuby wrapper around the Incanter library to provide > > nice and powerful functions to create plots and graphs for numerical > > and statistical analyses. > > Look at the specs to see what methods are available, but basically all > > the common plotting functions are covered, including image export in > > PNG, JPG or PDF format. There is also a "view" method that can let you > > open the graphs in real time and see what you are plotting, a nice > > function for scripts or IRB sessions. > > Even if you don't know Clojure that's not a problem, the gem takes > > care of everything and includes a ready to use Jar with both Clojure > > and Incanter. > > > > I think this kind of gems show how JRuby can facilitate the life of a > > bioinformatician, using existing solutions that just work and > > providing the best out of (Bio)Ruby and the JVM. > > > > -- > > > > Francesco > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > -- > -- > Ben Woodcroft > http://ecogenomic.org/users/ben-woodcroft > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From donttrustben at gmail.com Wed Aug 8 08:47:06 2012 From: donttrustben at gmail.com (Ben Woodcroft) Date: Wed, 8 Aug 2012 22:47:06 +1000 Subject: [BioRuby] Bio-Incanter In-Reply-To: References: Message-ID: On 8 August 2012 20:00, Matteo Picciolini wrote: > Hi guys . I write a simple wiki with two examples to use bio-incanter . > https://github.com/cerbero/bioruby-incanter/wiki > Enjoy ! > Cool, thanks. From lomereiter at gmail.com Mon Aug 20 05:47:18 2012 From: lomereiter at gmail.com (Artem Tarasov) Date: Mon, 20 Aug 2012 13:47:18 +0400 Subject: [BioRuby] GSoC final report Message-ID: Hi all, here's a wrap-up of what was added/fixed in sambamba and Ruby bindings during the last couple of weeks: http://lomereiter.wordpress.com/2012/08/20/gsoc-weekly-report-12/ * Tools don't require input files to be seekable anymore, allowing to work with e.g. /dev/stdin and /dev/stdout * I've added an option of MessagePack output, that drastically improved speed of bindings (2-4x speedup depending on configuration) * The gem is on Travis CI now, passing tests on MRI 1.9.2/1.9.3. (JRuby also works, but on Travis there're problems with popen, same as with BioRuby) * The tool 'sambamba_filter' is now available on Galaxy Tool Shed. It's been a great summer. Thank you OBF/BioRuby folks :) -- Artem From pjotr.public14 at thebird.nl Mon Aug 20 05:55:59 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 20 Aug 2012 11:55:59 +0200 Subject: [BioRuby] GSoC final report In-Reply-To: References: Message-ID: <20120820095559.GB2453@thebird.nl> Thank you Artem, Great job. Pj. On Mon, Aug 20, 2012 at 01:47:18PM +0400, Artem Tarasov wrote: > Hi all, > > here's a wrap-up of what was added/fixed in sambamba and Ruby bindings > during the last couple of weeks: > http://lomereiter.wordpress.com/2012/08/20/gsoc-weekly-report-12/ > > * Tools don't require input files to be seekable anymore, allowing to work > with e.g. /dev/stdin and /dev/stdout > * I've added an option of MessagePack output, that drastically improved > speed of bindings (2-4x speedup depending on configuration) > * The gem is on Travis CI now, passing tests on MRI 1.9.2/1.9.3. (JRuby > also works, but on Travis there're problems with popen, same as with > BioRuby) > * The tool 'sambamba_filter' is now available on Galaxy Tool Shed. > > > It's been a great summer. Thank you OBF/BioRuby folks :) > > > -- > Artem > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ngoto at gen-info.osaka-u.ac.jp Tue Aug 21 12:37:46 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Wed, 22 Aug 2012 01:37:46 +0900 Subject: [BioRuby] BioRuby 1.4.3 released Message-ID: <201208211644.q7LGiVsb026407@portal.open-bio.org> Hi, all, We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius. Tar.gz file: http://bioruby.org/archive/bioruby-1.4.3.tar.gz Gem file: http://bioruby.org/archive/gems/bio-1.4.3.gem We also put RubyGems pacakge at RubyGems.org and RubyForge (*). (* Files on RubyForge will soon be available.) You can easily install by using RubyGems. First, check the version number by using search command: % gem search --remote bio and find ?bio (1.4.3)? in the list. Then, % sudo gem install bio Here is a brief summary of changes. * Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for storing a graphics element. * Many failures and errors running on JRuby and Rubinius are resolved. * Strange behavior related with ?circular require? is fixed. * Fixed: Genomenet remote BLAST does not work. * Fixed: Bio::NucleicAcid.to_re(?s?) typo. * Fixed: Bio::EMBL#os raises RuntimeError. * Fixed: bin/bioruby: Failed to save object with error message "can?t convert Symbol into String" on Ruby 1.9. In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog. Acknowledgments: Thanks to all persons reporting issues and/or submitting patches. Hope you enjoy. P.S. We are having trouble when updating http://bioruby.org/ and http://bioruby.open-bio.org/ webpages now, possibly because of file/directory permissions in open-bio.org server. -- Naohisa Goto ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp From marian.povolny at gmail.com Tue Aug 21 15:11:01 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Tue, 21 Aug 2012 21:11:01 +0200 Subject: [BioRuby] Final GSoC report Message-ID: http://blog.mpthecoder.com/post/29910330225/final-gsoc-report *Summary* Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the end of the summer. At least in GSoC terms. Should I say end of the project? I don?t think so. The tools can still be improved, and the Ruby bindings should follow. The major changes since the last release include the following: - filtering functionality has been moved to a separate utility: gff3-filter, along with a new language for specifying filtering expressions, - conversion to table format of selected fields has been moved to a separate utility: gff3-select. However, the ?select option is still part of gff3-filter, - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA files for CDS and mRNA records and features, - man pages for utilities. ** The original idea was to create a GFF3/GTF parser in D and Ruby bindings. The Ruby bindings part didn?t work out because there is still no support for D shared libraries in Linux, but instead there are now a few useful command-line tools for processing GFF3 which can be used without programming knowledge. To me, the summer was fun, challenging, and a great experience. I even got to meet my mentor in person, and other community members too, and to make my first steps in bioinformatics. I even gave a small presentation at the EU-codefest. What a summer it was! Thanks to everybody who made it possible: Google, Open Bioinformatics Foundation and my mentor Pjotr Prins. -- Marjan From cswh at umich.edu Tue Aug 21 15:35:21 2012 From: cswh at umich.edu (Clayton Wheeler) Date: Tue, 21 Aug 2012 12:35:21 -0700 Subject: [BioRuby] Bio-MAF 1.0.1 Message-ID: Hi all, I've released bio-maf 1.0.1 and written a final GSoC blog post about it: http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ This release should be substantially more robust, with solid and reasonably-performing BGZF support, better CLI tools, and various robustness, compatibility, and memory-footprint improvements. (I've also developed a Galaxy integration for the maf_tile tool; unlike the existing Galaxy MAF tools, this is capable of filling in gaps with a FASTA reference sequence, and concatenating the alignment output from several exons specified in a BED file. It's not quite all packaged up with the toolshed facility yet, but I should be able to wrap that up shortly. Sneak preview: https://gist.github.com/3418576) It's been a pleasure working with all of you, and I'm glad I've been able to deliver something useful. Pjotr, Raoul, Francesco, thanks for your help and advice this summer! Marjan, Artem, you guys did excellent work and gave me some great suggestions in the code reviews. And, of course, thanks to Google for organizing and funding this! -- Clayton Wheeler cswh at umich.edu From pjotr.public14 at thebird.nl Tue Aug 21 17:47:53 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 21 Aug 2012 23:47:53 +0200 Subject: [BioRuby] Bio-MAF 1.0.1 In-Reply-To: References: Message-ID: <20120821214753.GB10348@thebird.nl> Thank you Marjan and Clayton. It was our pleasure. Pj. On Tue, Aug 21, 2012 at 12:35:21PM -0700, Clayton Wheeler wrote: > Hi all, > > I've released bio-maf 1.0.1 and written a final GSoC blog post about it: > > http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ > > This release should be substantially more robust, with solid and > reasonably-performing BGZF support, better CLI tools, and various > robustness, compatibility, and memory-footprint improvements. > > (I've also developed a Galaxy integration for the maf_tile tool; > unlike the existing Galaxy MAF tools, this is capable of filling in > gaps with a FASTA reference sequence, and concatenating the alignment > output from several exons specified in a BED file. It's not quite all > packaged up with the toolshed facility yet, but I should be able to > wrap that up shortly. Sneak preview: https://gist.github.com/3418576) > > It's been a pleasure working with all of you, and I'm glad I've been > able to deliver something useful. Pjotr, Raoul, Francesco, thanks for > your help and advice this summer! Marjan, Artem, you guys did > excellent work and gave me some great suggestions in the code reviews. > And, of course, thanks to Google for organizing and funding this! > > -- > Clayton Wheeler > cswh at umich.edu > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From mail at michaelbarton.me.uk Tue Aug 21 19:01:26 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 21 Aug 2012 19:01:26 -0400 Subject: [BioRuby] Bio-MAF 1.0.1 In-Reply-To: <20120821214753.GB10348@thebird.nl> References: <20120821214753.GB10348@thebird.nl> Message-ID: <20120821230126.GA22019@bartonh-mbp-01.mcd31065.det.wayport.net> Yes, great work by both of you. I've enjoyed reading your blog posts and it has great to see two bioinformaticians developing. Perhaps this may be obvious, I think it is worth reiterating though: be sure to highlight this work when applying for future positions. This is a great addition to your resume/CV. Thanks also to the BioRuby members who have committed their time to organising and mentoring during this GSOC. Mike On Tue, Aug 21, 2012 at 11:47:53PM +0200, Pjotr Prins wrote: > Thank you Marjan and Clayton. It was our pleasure. > > Pj. > > On Tue, Aug 21, 2012 at 12:35:21PM -0700, Clayton Wheeler wrote: > > > Hi all, > > > > I've released bio-maf 1.0.1 and written a final GSoC blog post about > > it: > > > > http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ > > > > This release should be substantially more robust, with solid and > > reasonably-performing BGZF support, better CLI tools, and various > > robustness, compatibility, and memory-footprint improvements. > > > > (I've also developed a Galaxy integration for the maf_tile tool; > > unlike the existing Galaxy MAF tools, this is capable of filling > > in gaps with a FASTA reference sequence, and concatenating > > the alignment output from several exons specified in a BED > > file. It's not quite all packaged up with the toolshed facility > > yet, but I should be able to wrap that up shortly. Sneak preview: > > https://gist.github.com/3418576) > > > > It's been a pleasure working with all of you, and I'm glad I've > > been able to deliver something useful. Pjotr, Raoul, Francesco, > > thanks for your help and advice this summer! Marjan, Artem, you > > guys did excellent work and gave me some great suggestions in the > > code reviews. And, of course, thanks to Google for organizing and > > funding this! > > > > -- Clayton Wheeler cswh at umich.edu > > ____________________________________________________________________ > > 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 mictadlo at gmail.com Tue Aug 21 20:55:30 2012 From: mictadlo at gmail.com (Mic) Date: Wed, 22 Aug 2012 10:55:30 +1000 Subject: [BioRuby] Final GSoC report In-Reply-To: References: Message-ID: Hi, Python is able to connect to D with help of http://pyd.dsource.org/ . Maybe it would be something for Biopython Cheers, Mic On Wed, Aug 22, 2012 at 5:11 AM, Marjan Povolni wrote: > http://blog.mpthecoder.com/post/29910330225/final-gsoc-report > > *Summary* > > Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the end > of the summer. At least in GSoC terms. Should I say end of the project? I > don?t think so. The tools can still be improved, and the Ruby bindings > should follow. > > The major changes since the last release include the following: > > - filtering functionality has been moved to a separate utility: > gff3-filter, along with a new language for specifying filtering > expressions, > - conversion to table format of selected fields has been moved to a > separate utility: gff3-select. However, the ?select option is still > part of > gff3-filter, > - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA files > for CDS and mRNA records and features, > - man pages for utilities. > > ** > The original idea was to create a GFF3/GTF parser in D and Ruby bindings. > The Ruby bindings part didn?t work out because there is still no support > for D shared libraries in Linux, but instead there are now a few useful > command-line tools for processing GFF3 which can be used without > programming knowledge. > > To me, the summer was fun, challenging, and a great experience. I even got > to meet my mentor in person, and other community members too, and to make > my first steps in bioinformatics. I even gave a small presentation at the > EU-codefest. What a summer it was! > > Thanks to everybody who made it possible: Google, Open Bioinformatics > Foundation and my mentor Pjotr Prins. > > -- > Marjan > > _______________________________________________ > 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 Wed Aug 22 00:16:13 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 22 Aug 2012 04:16:13 +0000 Subject: [BioRuby] GSoC final report In-Reply-To: <20120820095559.GB2453@thebird.nl> References: <20120820095559.GB2453@thebird.nl> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF33B73325@CHIMBX5.ad.uillinois.edu> Wholeheartedly agree. Congrats Artem on a job well done! chris On Aug 20, 2012, at 4:55 AM, Pjotr Prins wrote: > Thank you Artem, > > Great job. > > Pj. > > On Mon, Aug 20, 2012 at 01:47:18PM +0400, Artem Tarasov wrote: >> Hi all, >> >> here's a wrap-up of what was added/fixed in sambamba and Ruby bindings >> during the last couple of weeks: >> http://lomereiter.wordpress.com/2012/08/20/gsoc-weekly-report-12/ >> >> * Tools don't require input files to be seekable anymore, allowing to work >> with e.g. /dev/stdin and /dev/stdout >> * I've added an option of MessagePack output, that drastically improved >> speed of bindings (2-4x speedup depending on configuration) >> * The gem is on Travis CI now, passing tests on MRI 1.9.2/1.9.3. (JRuby >> also works, but on Travis there're problems with popen, same as with >> BioRuby) >> * The tool 'sambamba_filter' is now available on Galaxy Tool Shed. >> >> >> It's been a great summer. Thank you OBF/BioRuby folks :) >> >> >> -- >> Artem >> _______________________________________________ >> 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 georgkam at gmail.com Wed Aug 22 01:54:46 2012 From: georgkam at gmail.com (George Githinji) Date: Wed, 22 Aug 2012 08:54:46 +0300 Subject: [BioRuby] BioRuby 1.4.3 released In-Reply-To: <201208211644.q7LGiVsb026407@portal.open-bio.org> References: <201208211644.q7LGiVsb026407@portal.open-bio.org> Message-ID: Hi Thank you for all the bug fixes and the hard work. On Tue, Aug 21, 2012 at 7:37 PM, Naohisa GOTO wrote: > Hi, all, > > We are pleased to announce the release of BioRuby 1.4.3. > This new release fixes bugs existed in 1.4.2 and improves > portability on JRuby and Rubinius. > > Tar.gz file: http://bioruby.org/archive/bioruby-1.4.3.tar.gz > Gem file: http://bioruby.org/archive/gems/bio-1.4.3.gem > > We also put RubyGems pacakge at RubyGems.org and RubyForge (*). > (* Files on RubyForge will soon be available.) > > You can easily install by using RubyGems. First, check the > version number by using search command: > % gem search --remote bio > and find ?bio (1.4.3)? in the list. Then, > % sudo gem install bio > > Here is a brief summary of changes. > > * Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics > for storing a graphics element. > * Many failures and errors running on JRuby and Rubinius are resolved. > * Strange behavior related with ?circular require? is fixed. > * Fixed: Genomenet remote BLAST does not work. > * Fixed: Bio::NucleicAcid.to_re(?s?) typo. > * Fixed: Bio::EMBL#os raises RuntimeError. > * Fixed: bin/bioruby: Failed to save object with error message > "can?t convert Symbol into String" on Ruby 1.9. > > In addition, many changes have been made, including incompatible > changes. For more information, see RELEASE_NOTES.rdoc and > ChangeLog. > > Acknowledgments: Thanks to all persons reporting issues and/or > submitting patches. > > Hope you enjoy. > > P.S. We are having trouble when updating http://bioruby.org/ > and http://bioruby.open-bio.org/ webpages now, possibly because > of file/directory permissions in open-bio.org server. > > -- > Naohisa Goto > ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From lomereiter at gmail.com Wed Aug 22 02:42:12 2012 From: lomereiter at gmail.com (Artem Tarasov) Date: Wed, 22 Aug 2012 10:42:12 +0400 Subject: [BioRuby] [GSoC] Final GSoC report In-Reply-To: References: Message-ID: Hi, Unfortunately, the problem is on the side of D. PyD wiki ( https://bitbucket.org/ariovistus/pyd/wiki/Home) says that "extension libraries are nominally working with LDC (FE 2.060 or later); however, druntime currently limits what can be done here". However, this issue has become quite popular in last months, see e.g. this thread: http://forum.dlang.org/thread/mailman.1330.1345434177.31962.digitalmars-d at puremagic.com ? so maybe this'll get fixed soon. -- Artem On Wed, Aug 22, 2012 at 4:55 AM, Mic wrote: > Hi, > Python is able to connect to D with help of http://pyd.dsource.org/ . > > Maybe it would be something for Biopython > > Cheers, > Mic > > On Wed, Aug 22, 2012 at 5:11 AM, Marjan Povolni >wrote: > > > http://blog.mpthecoder.com/post/29910330225/final-gsoc-report > > > > *Summary* > > > > Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the > end > > of the summer. At least in GSoC terms. Should I say end of the project? I > > don?t think so. The tools can still be improved, and the Ruby bindings > > should follow. > > > > The major changes since the last release include the following: > > > > - filtering functionality has been moved to a separate utility: > > gff3-filter, along with a new language for specifying filtering > > expressions, > > - conversion to table format of selected fields has been moved to a > > separate utility: gff3-select. However, the ?select option is still > > part of > > gff3-filter, > > - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA > files > > for CDS and mRNA records and features, > > - man pages for utilities. > > > > ** > > The original idea was to create a GFF3/GTF parser in D and Ruby bindings. > > The Ruby bindings part didn?t work out because there is still no support > > for D shared libraries in Linux, but instead there are now a few useful > > command-line tools for processing GFF3 which can be used without > > programming knowledge. > > > > To me, the summer was fun, challenging, and a great experience. I even > got > > to meet my mentor in person, and other community members too, and to make > > my first steps in bioinformatics. I even gave a small presentation at the > > EU-codefest. What a summer it was! > > > > Thanks to everybody who made it possible: Google, Open Bioinformatics > > Foundation and my mentor Pjotr Prins. > > > > -- > > Marjan > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc > From francesco.strozzi at gmail.com Wed Aug 22 03:33:49 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Wed, 22 Aug 2012 09:33:49 +0200 Subject: [BioRuby] Bio-MAF 1.0.1 In-Reply-To: <20120821230126.GA22019@bartonh-mbp-01.mcd31065.det.wayport.net> References: <20120821214753.GB10348@thebird.nl> <20120821230126.GA22019@bartonh-mbp-01.mcd31065.det.wayport.net> Message-ID: Artem, Marjan, Clayton, you all did a great job, it was a pleasure to follow your progresses as a co-mentor and clearly you achieved all the goals for your projects. Your tools are already on my personal list and will be used in production in the next months on our facility here in Italy. Thanks for all the hard work and I hope you will stay in contact and contribute again with the community and the BioRuby people! Francesco On Wed, Aug 22, 2012 at 1:01 AM, Michael Barton wrote: > Yes, great work by both of you. I've enjoyed reading your blog posts and it has > great to see two bioinformaticians developing. Perhaps this may be obvious, I > think it is worth reiterating though: be sure to highlight this work when > applying for future positions. This is a great addition to your resume/CV. > > Thanks also to the BioRuby members who have committed their time to organising > and mentoring during this GSOC. > > Mike > > On Tue, Aug 21, 2012 at 11:47:53PM +0200, Pjotr Prins wrote: > >> Thank you Marjan and Clayton. It was our pleasure. >> >> Pj. >> >> On Tue, Aug 21, 2012 at 12:35:21PM -0700, Clayton Wheeler wrote: >> >> > Hi all, >> > >> > I've released bio-maf 1.0.1 and written a final GSoC blog post about >> > it: >> > >> > http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ >> > >> > This release should be substantially more robust, with solid and >> > reasonably-performing BGZF support, better CLI tools, and various >> > robustness, compatibility, and memory-footprint improvements. >> > >> > (I've also developed a Galaxy integration for the maf_tile tool; >> > unlike the existing Galaxy MAF tools, this is capable of filling >> > in gaps with a FASTA reference sequence, and concatenating >> > the alignment output from several exons specified in a BED >> > file. It's not quite all packaged up with the toolshed facility >> > yet, but I should be able to wrap that up shortly. Sneak preview: >> > https://gist.github.com/3418576) >> > >> > It's been a pleasure working with all of you, and I'm glad I've >> > been able to deliver something useful. Pjotr, Raoul, Francesco, >> > thanks for your help and advice this summer! Marjan, Artem, you >> > guys did excellent work and gave me some great suggestions in the >> > code reviews. And, of course, thanks to Google for organizing and >> > funding this! >> > >> > -- Clayton Wheeler cswh at umich.edu >> > ____________________________________________________________________ >> > 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 > > _______________________________________________ > 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 Aug 22 06:43:52 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 22 Aug 2012 12:43:52 +0200 Subject: [BioRuby] [GSoC] Final GSoC report In-Reply-To: References: Message-ID: <20120822104352.GA11847@thebird.nl> Yes, linking to D from an interpreted language is not hard, basically it is the same calling convention as that of C. So a D shared library looks the same as a C shared library to the calling code - all existing foreign function interfaces (FFI) work. That is the good news. The bad news, as Artem points out, is that there is a problem in the D garbage collector. Items get collected, which should not. This will be fixed sooner or later. The commitment is there, and it is moving up the priority list. For us it did not matter, as the parsers and tools happily run on their own using a command line interface, without much overhead. One advantage, from my perspective, is that we are not tied to Ruby, at this point, and the tools can be hosted in Galaxy. Another advantage, perhaps, is that we have not been side-tracked in providing rich library interfaces. That appeals to my purist side. Writing FFI bindings later is not a problem. Pj. On Wed, Aug 22, 2012 at 10:42:12AM +0400, Artem Tarasov wrote: > Hi, > > Unfortunately, the problem is on the side of D. PyD wiki ( > https://bitbucket.org/ariovistus/pyd/wiki/Home) says that "extension > libraries are nominally working with LDC (FE 2.060 or later); however, > druntime currently limits what can be done here". > > However, this issue has become quite popular in last months, see e.g. this > thread: > http://forum.dlang.org/thread/mailman.1330.1345434177.31962.digitalmars-d at puremagic.com > ? > so maybe this'll get fixed soon. > > -- > Artem > > On Wed, Aug 22, 2012 at 4:55 AM, Mic wrote: > > > Hi, > > Python is able to connect to D with help of http://pyd.dsource.org/ . > > > > Maybe it would be something for Biopython > > > > Cheers, > > Mic > > > > On Wed, Aug 22, 2012 at 5:11 AM, Marjan Povolni > >wrote: > > > > > http://blog.mpthecoder.com/post/29910330225/final-gsoc-report > > > > > > *Summary* > > > > > > Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the > > end > > > of the summer. At least in GSoC terms. Should I say end of the project? I > > > don?t think so. The tools can still be improved, and the Ruby bindings > > > should follow. > > > > > > The major changes since the last release include the following: > > > > > > - filtering functionality has been moved to a separate utility: > > > gff3-filter, along with a new language for specifying filtering > > > expressions, > > > - conversion to table format of selected fields has been moved to a > > > separate utility: gff3-select. However, the ?select option is still > > > part of > > > gff3-filter, > > > - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA > > files > > > for CDS and mRNA records and features, > > > - man pages for utilities. > > > > > > ** > > > The original idea was to create a GFF3/GTF parser in D and Ruby bindings. > > > The Ruby bindings part didn?t work out because there is still no support > > > for D shared libraries in Linux, but instead there are now a few useful > > > command-line tools for processing GFF3 which can be used without > > > programming knowledge. > > > > > > To me, the summer was fun, challenging, and a great experience. I even > > got > > > to meet my mentor in person, and other community members too, and to make > > > my first steps in bioinformatics. I even gave a small presentation at the > > > EU-codefest. What a summer it was! > > > > > > Thanks to everybody who made it possible: Google, Open Bioinformatics > > > Foundation and my mentor Pjotr Prins. > > > > > > -- > > > Marjan > > > > > > _______________________________________________ > > > BioRuby Project - http://www.bioruby.org/ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > _______________________________________________ > > GSoC mailing list > > GSoC at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/gsoc > > > > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc From p.j.a.cock at googlemail.com Wed Aug 22 07:10:56 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 22 Aug 2012 12:10:56 +0100 Subject: [BioRuby] [GSoC] Final GSoC report In-Reply-To: <20120822104352.GA11847@thebird.nl> References: <20120822104352.GA11847@thebird.nl> Message-ID: On Wed, Aug 22, 2012 at 11:43 AM, Pjotr Prins wrote: > Yes, linking to D from an interpreted language is not hard, basically > it is the same calling convention as that of C. So a D shared library > looks the same as a C shared library to the calling code - all > existing foreign function interfaces (FFI) work. That is the good > news. How do things stand from a cross-platform perspective? i.e. When might this be doable on Linux, Mac OS X, and Windows? (and other Unix like platforms of potential interest) > The bad news, as Artem points out, is that there is a problem in the > D garbage collector. Items get collected, which should not. This will > be fixed sooner or later. The commitment is there, and it is moving > up the priority list. Is there a D issue/bug tracker for this? Thanks, Peter From cjfields at illinois.edu Wed Aug 22 08:46:37 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 22 Aug 2012 12:46:37 +0000 Subject: [BioRuby] Bio-MAF 1.0.1 In-Reply-To: References: <20120821214753.GB10348@thebird.nl> <20120821230126.GA22019@bartonh-mbp-01.mcd31065.det.wayport.net> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF33B73926@CHIMBX5.ad.uillinois.edu> I agree. I think this is likely the most successful of the GSoC runs I've seen. It definitely sets the bar high for the future. chris On Aug 22, 2012, at 2:33 AM, Francesco Strozzi wrote: > Artem, Marjan, Clayton, > > you all did a great job, it was a pleasure to follow your progresses > as a co-mentor and clearly you achieved all the goals for your > projects. Your tools are already on my personal list and will be used > in production in the next months on our facility here in Italy. > > Thanks for all the hard work and I hope you will stay in contact and > contribute again with the community and the BioRuby people! > > Francesco > > On Wed, Aug 22, 2012 at 1:01 AM, Michael Barton > wrote: >> Yes, great work by both of you. I've enjoyed reading your blog posts and it has >> great to see two bioinformaticians developing. Perhaps this may be obvious, I >> think it is worth reiterating though: be sure to highlight this work when >> applying for future positions. This is a great addition to your resume/CV. >> >> Thanks also to the BioRuby members who have committed their time to organising >> and mentoring during this GSOC. >> >> Mike >> >> On Tue, Aug 21, 2012 at 11:47:53PM +0200, Pjotr Prins wrote: >> >>> Thank you Marjan and Clayton. It was our pleasure. >>> >>> Pj. >>> >>> On Tue, Aug 21, 2012 at 12:35:21PM -0700, Clayton Wheeler wrote: >>> >>>> Hi all, >>>> >>>> I've released bio-maf 1.0.1 and written a final GSoC blog post about >>>> it: >>>> >>>> http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ >>>> >>>> This release should be substantially more robust, with solid and >>>> reasonably-performing BGZF support, better CLI tools, and various >>>> robustness, compatibility, and memory-footprint improvements. >>>> >>>> (I've also developed a Galaxy integration for the maf_tile tool; >>>> unlike the existing Galaxy MAF tools, this is capable of filling >>>> in gaps with a FASTA reference sequence, and concatenating >>>> the alignment output from several exons specified in a BED >>>> file. It's not quite all packaged up with the toolshed facility >>>> yet, but I should be able to wrap that up shortly. Sneak preview: >>>> https://gist.github.com/3418576) >>>> >>>> It's been a pleasure working with all of you, and I'm glad I've >>>> been able to deliver something useful. Pjotr, Raoul, Francesco, >>>> thanks for your help and advice this summer! Marjan, Artem, you >>>> guys did excellent work and gave me some great suggestions in the >>>> code reviews. And, of course, thanks to Google for organizing and >>>> funding this! >>>> >>>> -- Clayton Wheeler cswh at umich.edu >>>> ____________________________________________________________________ >>>> 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 >> >> _______________________________________________ >> 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 marian.povolny at gmail.com Wed Aug 1 12:46:44 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Wed, 1 Aug 2012 14:46:44 +0200 Subject: [BioRuby] GSoC weekly status report No.9 Message-ID: http://blog.mpthecoder.com/post/28481171942/gsoc-weekly-status-report-no-9 The trip to Lodi was very fruitful. It was great to meet both my mentor and other community members. Based on the input received at the codefest, I created a new plan for the second part of the summer: https://github.com/mamarjan/gff3-pltools/wiki/Part2 Since then I have done the following: - improved validation speed, - added GTF support for input and output, - table output with an option to select which fields and attributes should be in the table, - tools for conversion to GTF and JSON, - JSON output support, which needs some more polish. -- Marjan From pjotr.public14 at thebird.nl Sat Aug 4 11:07:42 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 4 Aug 2012 13:07:42 +0200 Subject: [BioRuby] BioRuby passes tests (kinda)! Message-ID: <20120804110742.GA7701@thebird.nl> Anyone noticed that BioRuby has gone green on http://biogems.info/? Not all tests pass, but Travis has a new function for telling it what versions of Ruby are *allowed* to fail. Heh. Be good when JRuby1.9 starts passing. Pj. From p.j.a.cock at googlemail.com Sat Aug 4 13:29:59 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 4 Aug 2012 14:29:59 +0100 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: <20120804110742.GA7701@thebird.nl> References: <20120804110742.GA7701@thebird.nl> Message-ID: On Sat, Aug 4, 2012 at 12:07 PM, Pjotr Prins wrote: > Anyone noticed that BioRuby has gone green on http://biogems.info/? > No - but I did notice it on the recent blog post: http://news.open-bio.org/news/2012/07/travis-ci-for-testing/ > Not all tests pass, but Travis has a new function for telling it what > versions of Ruby are *allowed* to fail. > > Heh. Good plan. > Be good when JRuby1.9 starts passing. > Do you know what the general problem is? Peter From ngoto at gen-info.osaka-u.ac.jp Sat Aug 4 15:48:54 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Sun, 05 Aug 2012 00:48:54 +0900 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: References: <20120804110742.GA7701@thebird.nl> Message-ID: <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> Hi, > On Sat, Aug 4, 2012 at 12:07 PM, Pjotr Prins wrote: > > Anyone noticed that BioRuby has gone green on http://biogems.info/? I've changed .travis.yml yesterday. https://github.com/bioruby/bioruby/commit/9a2fe67c247cdc7c9ddc9f8b8de771515ba76ac1 After the change, the status has been shown as "green". Keeping "green" status is important for using the automatic testing of pull requests by Travis-CI. On Sat, 4 Aug 2012 14:29:59 +0100, Peter Cock wrote: > No - but I did notice it on the recent blog post: > http://news.open-bio.org/news/2012/07/travis-ci-for-testing/ Thanks. > > Be good when JRuby1.9 starts passing. > > Do you know what the general problem is? I think some of them might be due to bugs in JRuby, but further investigation is needed. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From ngoto at gen-info.osaka-u.ac.jp Sat Aug 4 16:37:13 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Sun, 05 Aug 2012 01:37:13 +0900 Subject: [BioRuby] BioRuby 1.4.3 will soon be released Message-ID: <20120805013713.18B0.EEF6E030@gen-info.osaka-u.ac.jp> Hi all, I'd like to release a new version of BioRuby, BioRuby 1.4.3. This is minor maintainance release, mostly consisted of bug fixes. The new version also improves of portability running on Jruby and Rubinius. In the new version, little incompatible changes are made due to the side effects of some bug fixes. See RELEASE_NOTES.rdoc for more information (work in progress) https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc If you have any comments (or objections), please respond soon. I'd like to relase it in hurry, because almost 1 year has passed since the last release of 1.4.2. Note that the aim of the new version is bug fix. After the release, some new features may be added and some incompatible drastic changes may be made. Thanks, -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From cswh at umich.edu Sat Aug 4 16:42:21 2012 From: cswh at umich.edu (Clayton Wheeler) Date: Sat, 4 Aug 2012 12:42:21 -0400 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> References: <20120804110742.GA7701@thebird.nl> <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Sat, Aug 4, 2012 at 11:48 AM, Naohisa Goto wrote: > Hi, > >> On Sat, Aug 4, 2012 at 12:07 PM, Pjotr Prins wrote: >> > Anyone noticed that BioRuby has gone green on http://biogems.info/? > > I've changed .travis.yml yesterday. > https://github.com/bioruby/bioruby/commit/9a2fe67c247cdc7c9ddc9f8b8de771515ba76ac1 > After the change, the status has been shown as "green". > > Keeping "green" status is important for using the automatic testing of > pull requests by Travis-CI. > > On Sat, 4 Aug 2012 14:29:59 +0100, Peter Cock > wrote: >> No - but I did notice it on the recent blog post: >> http://news.open-bio.org/news/2012/07/travis-ci-for-testing/ > > Thanks. > >> > Be good when JRuby1.9 starts passing. >> >> Do you know what the general problem is? > > I think some of them might be due to bugs in JRuby, but > further investigation is needed. One of the JRuby bugs I filed on the basis of our test failures has been fixed, and that fix will be out in the next 1.7 preview release if it's not in the current one. Another (an autoload bug causing quite a few failures) has a fix that hasn't been integrated yet; I'll see if I can get that in for 1.7.0.preview2. Also, I've seen quite a few failures involving PhyloXML (particularly on JRuby); now that I've repackaged that as a bio-phyloxml gem (https://github.com/csw/bioruby-phyloxml, which is passing its tests on Travis-CI), we could think about removing it from the main BioRuby repository. -- Clayton Wheeler cswh at umich.edu From ngoto at gen-info.osaka-u.ac.jp Sun Aug 5 07:17:38 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Sun, 5 Aug 2012 16:17:38 +0900 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: References: <20120804110742.GA7701@thebird.nl> <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <201208050717.q757HdJR010728@portal.open-bio.org> On Sat, 4 Aug 2012 12:42:21 -0400 Clayton Wheeler wrote: > Also, I've seen quite a few failures involving PhyloXML (particularly > on JRuby); now that I've repackaged that as a bio-phyloxml gem > (https://github.com/csw/bioruby-phyloxml, which is passing its tests > on Travis-CI), we could think about removing it from the main BioRuby > repository. I'm againt to remove PhyloXML parts from the main repository only because the tests show many failures on JRuby. It runs without errors and errors on MRI (1.8.7, 1.9.2, 1.9.3) and Rubinius (1.8 mode). Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From cswh at umich.edu Sun Aug 5 23:24:58 2012 From: cswh at umich.edu (Clayton Wheeler) Date: Sun, 5 Aug 2012 19:24:58 -0400 Subject: [BioRuby] bio-maf update: BGZF and testing Message-ID: Hi all, I've posted an update on my most recent work on bio-maf. Highlights include BGZF compression support, a new maf_extract command-line tool for random access, and my discoveries from testing on the full UCSC multiz46way dataset. http://csw.github.com/bioruby-maf/blog/2012/08/05/bgzf_and_testing/ -- Clayton Wheeler cswh at umich.edu From lomereiter at gmail.com Mon Aug 6 10:33:54 2012 From: lomereiter at gmail.com (Artem Tarasov) Date: Mon, 6 Aug 2012 14:33:54 +0400 Subject: [BioRuby] [ruby code quality] Code Climate Message-ID: Hi all, Today I've stumbled upon github_api gem, and there is a badge next to Travis CI one, linking to Code Climate. As it turned out, Code Climate is a static analysis tool for Ruby code which helps to find various code smells. Less than a month ago they made their service free for github users: http://blog.codeclimate.com/blog/2012/07/10/code-climate-is-free-for-open-source/ As far as I understand, code analysis is done weekly (not on each push, like Travis CI), and notification is sent via email. IMHO everyone should go and use it :) From lomereiter at gmail.com Tue Aug 7 05:14:02 2012 From: lomereiter at gmail.com (Artem Tarasov) Date: Tue, 7 Aug 2012 05:14:02 +0000 Subject: [BioRuby] [GSoC] weekly report #11 Message-ID: Hello all, here's my latest report about work on sambamba: http://lomereiter.wordpress.com/2012/08/06/gsoc-weekly-report-11/ * simple internal DSL for filtering was introduced in bindings (description: https://github.com/lomereiter/bioruby-sambamba/blob/master/features/filtering.feature ) * BAM output support was added to filtering tool (sambamba view) * man pages for all tools were created * a script was written for building Debian packages and uploading them to Github * Debian packages for v0.2.1 are added to Github downloads (for both i386 and amd64) Now the goal is to make those tools accessible at Galaxy Tool Shed, and also this week I plan to optimize memory usage -- buffer sizes are quite large now, and the task is to find out how much they can be reduced without significant impact on performance. From pjotr.public14 at thebird.nl Tue Aug 7 10:42:24 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 7 Aug 2012 12:42:24 +0200 Subject: [BioRuby] BioRuby passes tests (kinda)! In-Reply-To: <201208050717.q757HdJR010728@portal.open-bio.org> References: <20120804110742.GA7701@thebird.nl> <20120805004853.18AD.EEF6E030@gen-info.osaka-u.ac.jp> <201208050717.q757HdJR010728@portal.open-bio.org> Message-ID: <20120807104224.GA25493@thebird.nl> On Sun, Aug 05, 2012 at 04:17:38PM +0900, Naohisa GOTO wrote: > On Sat, 4 Aug 2012 12:42:21 -0400 > Clayton Wheeler wrote: > > > Also, I've seen quite a few failures involving PhyloXML (particularly > > on JRuby); now that I've repackaged that as a bio-phyloxml gem > > (https://github.com/csw/bioruby-phyloxml, which is passing its tests > > on Travis-CI), we could think about removing it from the main BioRuby > > repository. > > I'm againt to remove PhyloXML parts from the main repository > only because the tests show many failures on JRuby. It runs > without errors and errors on MRI (1.8.7, 1.9.2, 1.9.3) and > Rubinius (1.8 mode). I agree the failing tests are not a reason for removing phyloxml. One thing we should discuss, however, is removing code from BioRuby when functional replacements exist, as it the case with bioruby-phyloxml. It makes little sense to maintain two source trees (even if they are phylo trees). Also, we may strip out parts of BioRuby which are not used anymore, or not-so-core, and push those out into biogems. That way BioRuby becomes 'lighter', easier to maintain and modify. That discussion we will have in Japan at the Biohackaton. Perhaps on the way to BioRuby 2.0, and even 3.0. Personally I am also developing ideas on what BioRuby should be, and what it should do. Currently I see the main use of the Bio* projects as being parsers and outputters of the pletora of Bioinformatics of data formats. Maybe we should stick to that, support any known input type, and generalized output, where output should at least support tabular output, JSON, XML, and RDF. All other stuff should go into biogems. Pj. From francesco.strozzi at gmail.com Tue Aug 7 13:23:53 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Tue, 7 Aug 2012 15:23:53 +0200 Subject: [BioRuby] Bio-Incanter Message-ID: Hi guys, after having played for a while with Clojure and Incanter (http://www.incanter.org/), we thought it was nice to have a Ruby gem to access such a great library, so I would like to point out a new BioGem called Bio-Incanter https://github.com/cerbero/bioruby-incanter . This gem was started by Matteo Picciolini, a bioinformatician working in my group here in Italy. He's at the first contribution in the BioRuby world, so be nice! The gem it's a JRuby wrapper around the Incanter library to provide nice and powerful functions to create plots and graphs for numerical and statistical analyses. Look at the specs to see what methods are available, but basically all the common plotting functions are covered, including image export in PNG, JPG or PDF format. There is also a "view" method that can let you open the graphs in real time and see what you are plotting, a nice function for scripts or IRB sessions. Even if you don't know Clojure that's not a problem, the gem takes care of everything and includes a ready to use Jar with both Clojure and Incanter. I think this kind of gems show how JRuby can facilitate the life of a bioinformatician, using existing solutions that just work and providing the best out of (Bio)Ruby and the JVM. -- Francesco From marian.povolny at gmail.com Tue Aug 7 13:36:04 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Tue, 7 Aug 2012 15:36:04 +0200 Subject: [BioRuby] GSoC weekly status report No.10 Message-ID: http://blog.mpthecoder.com/post/28907136767/gsoc-weekly-status-report-no-10 The 0.3 release is available on the website: http://mamarjan.github.com/gff3-pltools/ In addition to what was described in the last weekly report, a GFF3 sorting tool has been added, grouping records which belong to the same feature, and Ruby bindings have been updated to support GTF and new options in gff3-ffetch. -- Marjan From donttrustben at gmail.com Wed Aug 8 00:20:38 2012 From: donttrustben at gmail.com (Ben Woodcroft) Date: Wed, 8 Aug 2012 10:20:38 +1000 Subject: [BioRuby] Bio-Incanter In-Reply-To: References: Message-ID: Hi guys, sounds cool on the face of it to me, thanks. Congrats to Matteo. Annoyingly http://data-sorcery.org is being difficult to access for me. Any chance you could add a simple example(s) to the README or wiki? On 7 August 2012 23:23, Francesco Strozzi wrote: > Hi guys, > after having played for a while with Clojure and Incanter > (http://www.incanter.org/), we thought it was nice to have a Ruby gem > to access such a great library, so I would like to point out a new > BioGem called Bio-Incanter https://github.com/cerbero/bioruby-incanter > . > This gem was started by Matteo Picciolini, a bioinformatician working > in my group here in Italy. He's at the first contribution in the > BioRuby world, so be nice! > > The gem it's a JRuby wrapper around the Incanter library to provide > nice and powerful functions to create plots and graphs for numerical > and statistical analyses. > Look at the specs to see what methods are available, but basically all > the common plotting functions are covered, including image export in > PNG, JPG or PDF format. There is also a "view" method that can let you > open the graphs in real time and see what you are plotting, a nice > function for scripts or IRB sessions. > Even if you don't know Clojure that's not a problem, the gem takes > care of everything and includes a ready to use Jar with both Clojure > and Incanter. > > I think this kind of gems show how JRuby can facilitate the life of a > bioinformatician, using existing solutions that just work and > providing the best out of (Bio)Ruby and the JVM. > > -- > > Francesco > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- -- Ben Woodcroft http://ecogenomic.org/users/ben-woodcroft From donttrustben at gmail.com Wed Aug 8 07:23:21 2012 From: donttrustben at gmail.com (Ben Woodcroft) Date: Wed, 8 Aug 2012 17:23:21 +1000 Subject: [BioRuby] New biogems for ipcress, krona and small kmer counting Message-ID: More adverts.. bio-ipcress is a programmatic interface to exonerate's ipcress, an in-silico PCR system. https://github.com/wwood/bioruby-ipcress bio-krona is a programmatic interface to Krona, a HTML visualisation tool for hierarchical data. https://github.com/wwood/bioruby-krona bio-kmer_counter is a pure ruby gem for counting small kmers (e.g. 4mers) within sequences, for fingerprinting purposes e.g. the binning of metagenomic data. https://github.com/wwood/bioruby-kmer_counter Enjoy, ben -- -- Ben Woodcroft http://ecogenomic.org/users/ben-woodcroft From matteo.picciolini at gmail.com Wed Aug 8 10:00:44 2012 From: matteo.picciolini at gmail.com (Matteo Picciolini) Date: Wed, 8 Aug 2012 12:00:44 +0200 Subject: [BioRuby] Bio-Incanter In-Reply-To: References: Message-ID: Hi guys . I write a simple wiki with two examples to use bio-incanter . https://github.com/cerbero/bioruby-incanter/wiki Enjoy ! 2012/8/8 Ben Woodcroft > Hi guys, sounds cool on the face of it to me, thanks. Congrats to Matteo. > > Annoyingly http://data-sorcery.org is being difficult to access for me. > Any > chance you could add a simple example(s) to the README or wiki? > > On 7 August 2012 23:23, Francesco Strozzi >wrote: > > > Hi guys, > > after having played for a while with Clojure and Incanter > > (http://www.incanter.org/), we thought it was nice to have a Ruby gem > > to access such a great library, so I would like to point out a new > > BioGem called Bio-Incanter https://github.com/cerbero/bioruby-incanter > > . > > This gem was started by Matteo Picciolini, a bioinformatician working > > in my group here in Italy. He's at the first contribution in the > > BioRuby world, so be nice! > > > > The gem it's a JRuby wrapper around the Incanter library to provide > > nice and powerful functions to create plots and graphs for numerical > > and statistical analyses. > > Look at the specs to see what methods are available, but basically all > > the common plotting functions are covered, including image export in > > PNG, JPG or PDF format. There is also a "view" method that can let you > > open the graphs in real time and see what you are plotting, a nice > > function for scripts or IRB sessions. > > Even if you don't know Clojure that's not a problem, the gem takes > > care of everything and includes a ready to use Jar with both Clojure > > and Incanter. > > > > I think this kind of gems show how JRuby can facilitate the life of a > > bioinformatician, using existing solutions that just work and > > providing the best out of (Bio)Ruby and the JVM. > > > > -- > > > > Francesco > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > -- > -- > Ben Woodcroft > http://ecogenomic.org/users/ben-woodcroft > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From donttrustben at gmail.com Wed Aug 8 12:47:06 2012 From: donttrustben at gmail.com (Ben Woodcroft) Date: Wed, 8 Aug 2012 22:47:06 +1000 Subject: [BioRuby] Bio-Incanter In-Reply-To: References: Message-ID: On 8 August 2012 20:00, Matteo Picciolini wrote: > Hi guys . I write a simple wiki with two examples to use bio-incanter . > https://github.com/cerbero/bioruby-incanter/wiki > Enjoy ! > Cool, thanks. From lomereiter at gmail.com Mon Aug 20 09:47:18 2012 From: lomereiter at gmail.com (Artem Tarasov) Date: Mon, 20 Aug 2012 13:47:18 +0400 Subject: [BioRuby] GSoC final report Message-ID: Hi all, here's a wrap-up of what was added/fixed in sambamba and Ruby bindings during the last couple of weeks: http://lomereiter.wordpress.com/2012/08/20/gsoc-weekly-report-12/ * Tools don't require input files to be seekable anymore, allowing to work with e.g. /dev/stdin and /dev/stdout * I've added an option of MessagePack output, that drastically improved speed of bindings (2-4x speedup depending on configuration) * The gem is on Travis CI now, passing tests on MRI 1.9.2/1.9.3. (JRuby also works, but on Travis there're problems with popen, same as with BioRuby) * The tool 'sambamba_filter' is now available on Galaxy Tool Shed. It's been a great summer. Thank you OBF/BioRuby folks :) -- Artem From pjotr.public14 at thebird.nl Mon Aug 20 09:55:59 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 20 Aug 2012 11:55:59 +0200 Subject: [BioRuby] GSoC final report In-Reply-To: References: Message-ID: <20120820095559.GB2453@thebird.nl> Thank you Artem, Great job. Pj. On Mon, Aug 20, 2012 at 01:47:18PM +0400, Artem Tarasov wrote: > Hi all, > > here's a wrap-up of what was added/fixed in sambamba and Ruby bindings > during the last couple of weeks: > http://lomereiter.wordpress.com/2012/08/20/gsoc-weekly-report-12/ > > * Tools don't require input files to be seekable anymore, allowing to work > with e.g. /dev/stdin and /dev/stdout > * I've added an option of MessagePack output, that drastically improved > speed of bindings (2-4x speedup depending on configuration) > * The gem is on Travis CI now, passing tests on MRI 1.9.2/1.9.3. (JRuby > also works, but on Travis there're problems with popen, same as with > BioRuby) > * The tool 'sambamba_filter' is now available on Galaxy Tool Shed. > > > It's been a great summer. Thank you OBF/BioRuby folks :) > > > -- > Artem > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ngoto at gen-info.osaka-u.ac.jp Tue Aug 21 16:37:46 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Wed, 22 Aug 2012 01:37:46 +0900 Subject: [BioRuby] BioRuby 1.4.3 released Message-ID: <201208211644.q7LGiVsb026407@portal.open-bio.org> Hi, all, We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius. Tar.gz file: http://bioruby.org/archive/bioruby-1.4.3.tar.gz Gem file: http://bioruby.org/archive/gems/bio-1.4.3.gem We also put RubyGems pacakge at RubyGems.org and RubyForge (*). (* Files on RubyForge will soon be available.) You can easily install by using RubyGems. First, check the version number by using search command: % gem search --remote bio and find ?bio (1.4.3)? in the list. Then, % sudo gem install bio Here is a brief summary of changes. * Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for storing a graphics element. * Many failures and errors running on JRuby and Rubinius are resolved. * Strange behavior related with ?circular require? is fixed. * Fixed: Genomenet remote BLAST does not work. * Fixed: Bio::NucleicAcid.to_re(?s?) typo. * Fixed: Bio::EMBL#os raises RuntimeError. * Fixed: bin/bioruby: Failed to save object with error message "can?t convert Symbol into String" on Ruby 1.9. In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog. Acknowledgments: Thanks to all persons reporting issues and/or submitting patches. Hope you enjoy. P.S. We are having trouble when updating http://bioruby.org/ and http://bioruby.open-bio.org/ webpages now, possibly because of file/directory permissions in open-bio.org server. -- Naohisa Goto ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp From marian.povolny at gmail.com Tue Aug 21 19:11:01 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Tue, 21 Aug 2012 21:11:01 +0200 Subject: [BioRuby] Final GSoC report Message-ID: http://blog.mpthecoder.com/post/29910330225/final-gsoc-report *Summary* Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the end of the summer. At least in GSoC terms. Should I say end of the project? I don?t think so. The tools can still be improved, and the Ruby bindings should follow. The major changes since the last release include the following: - filtering functionality has been moved to a separate utility: gff3-filter, along with a new language for specifying filtering expressions, - conversion to table format of selected fields has been moved to a separate utility: gff3-select. However, the ?select option is still part of gff3-filter, - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA files for CDS and mRNA records and features, - man pages for utilities. ** The original idea was to create a GFF3/GTF parser in D and Ruby bindings. The Ruby bindings part didn?t work out because there is still no support for D shared libraries in Linux, but instead there are now a few useful command-line tools for processing GFF3 which can be used without programming knowledge. To me, the summer was fun, challenging, and a great experience. I even got to meet my mentor in person, and other community members too, and to make my first steps in bioinformatics. I even gave a small presentation at the EU-codefest. What a summer it was! Thanks to everybody who made it possible: Google, Open Bioinformatics Foundation and my mentor Pjotr Prins. -- Marjan From cswh at umich.edu Tue Aug 21 19:35:21 2012 From: cswh at umich.edu (Clayton Wheeler) Date: Tue, 21 Aug 2012 12:35:21 -0700 Subject: [BioRuby] Bio-MAF 1.0.1 Message-ID: Hi all, I've released bio-maf 1.0.1 and written a final GSoC blog post about it: http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ This release should be substantially more robust, with solid and reasonably-performing BGZF support, better CLI tools, and various robustness, compatibility, and memory-footprint improvements. (I've also developed a Galaxy integration for the maf_tile tool; unlike the existing Galaxy MAF tools, this is capable of filling in gaps with a FASTA reference sequence, and concatenating the alignment output from several exons specified in a BED file. It's not quite all packaged up with the toolshed facility yet, but I should be able to wrap that up shortly. Sneak preview: https://gist.github.com/3418576) It's been a pleasure working with all of you, and I'm glad I've been able to deliver something useful. Pjotr, Raoul, Francesco, thanks for your help and advice this summer! Marjan, Artem, you guys did excellent work and gave me some great suggestions in the code reviews. And, of course, thanks to Google for organizing and funding this! -- Clayton Wheeler cswh at umich.edu From pjotr.public14 at thebird.nl Tue Aug 21 21:47:53 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 21 Aug 2012 23:47:53 +0200 Subject: [BioRuby] Bio-MAF 1.0.1 In-Reply-To: References: Message-ID: <20120821214753.GB10348@thebird.nl> Thank you Marjan and Clayton. It was our pleasure. Pj. On Tue, Aug 21, 2012 at 12:35:21PM -0700, Clayton Wheeler wrote: > Hi all, > > I've released bio-maf 1.0.1 and written a final GSoC blog post about it: > > http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ > > This release should be substantially more robust, with solid and > reasonably-performing BGZF support, better CLI tools, and various > robustness, compatibility, and memory-footprint improvements. > > (I've also developed a Galaxy integration for the maf_tile tool; > unlike the existing Galaxy MAF tools, this is capable of filling in > gaps with a FASTA reference sequence, and concatenating the alignment > output from several exons specified in a BED file. It's not quite all > packaged up with the toolshed facility yet, but I should be able to > wrap that up shortly. Sneak preview: https://gist.github.com/3418576) > > It's been a pleasure working with all of you, and I'm glad I've been > able to deliver something useful. Pjotr, Raoul, Francesco, thanks for > your help and advice this summer! Marjan, Artem, you guys did > excellent work and gave me some great suggestions in the code reviews. > And, of course, thanks to Google for organizing and funding this! > > -- > Clayton Wheeler > cswh at umich.edu > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From mail at michaelbarton.me.uk Tue Aug 21 23:01:26 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 21 Aug 2012 19:01:26 -0400 Subject: [BioRuby] Bio-MAF 1.0.1 In-Reply-To: <20120821214753.GB10348@thebird.nl> References: <20120821214753.GB10348@thebird.nl> Message-ID: <20120821230126.GA22019@bartonh-mbp-01.mcd31065.det.wayport.net> Yes, great work by both of you. I've enjoyed reading your blog posts and it has great to see two bioinformaticians developing. Perhaps this may be obvious, I think it is worth reiterating though: be sure to highlight this work when applying for future positions. This is a great addition to your resume/CV. Thanks also to the BioRuby members who have committed their time to organising and mentoring during this GSOC. Mike On Tue, Aug 21, 2012 at 11:47:53PM +0200, Pjotr Prins wrote: > Thank you Marjan and Clayton. It was our pleasure. > > Pj. > > On Tue, Aug 21, 2012 at 12:35:21PM -0700, Clayton Wheeler wrote: > > > Hi all, > > > > I've released bio-maf 1.0.1 and written a final GSoC blog post about > > it: > > > > http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ > > > > This release should be substantially more robust, with solid and > > reasonably-performing BGZF support, better CLI tools, and various > > robustness, compatibility, and memory-footprint improvements. > > > > (I've also developed a Galaxy integration for the maf_tile tool; > > unlike the existing Galaxy MAF tools, this is capable of filling > > in gaps with a FASTA reference sequence, and concatenating > > the alignment output from several exons specified in a BED > > file. It's not quite all packaged up with the toolshed facility > > yet, but I should be able to wrap that up shortly. Sneak preview: > > https://gist.github.com/3418576) > > > > It's been a pleasure working with all of you, and I'm glad I've > > been able to deliver something useful. Pjotr, Raoul, Francesco, > > thanks for your help and advice this summer! Marjan, Artem, you > > guys did excellent work and gave me some great suggestions in the > > code reviews. And, of course, thanks to Google for organizing and > > funding this! > > > > -- Clayton Wheeler cswh at umich.edu > > ____________________________________________________________________ > > 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 mictadlo at gmail.com Wed Aug 22 00:55:30 2012 From: mictadlo at gmail.com (Mic) Date: Wed, 22 Aug 2012 10:55:30 +1000 Subject: [BioRuby] Final GSoC report In-Reply-To: References: Message-ID: Hi, Python is able to connect to D with help of http://pyd.dsource.org/ . Maybe it would be something for Biopython Cheers, Mic On Wed, Aug 22, 2012 at 5:11 AM, Marjan Povolni wrote: > http://blog.mpthecoder.com/post/29910330225/final-gsoc-report > > *Summary* > > Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the end > of the summer. At least in GSoC terms. Should I say end of the project? I > don?t think so. The tools can still be improved, and the Ruby bindings > should follow. > > The major changes since the last release include the following: > > - filtering functionality has been moved to a separate utility: > gff3-filter, along with a new language for specifying filtering > expressions, > - conversion to table format of selected fields has been moved to a > separate utility: gff3-select. However, the ?select option is still > part of > gff3-filter, > - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA files > for CDS and mRNA records and features, > - man pages for utilities. > > ** > The original idea was to create a GFF3/GTF parser in D and Ruby bindings. > The Ruby bindings part didn?t work out because there is still no support > for D shared libraries in Linux, but instead there are now a few useful > command-line tools for processing GFF3 which can be used without > programming knowledge. > > To me, the summer was fun, challenging, and a great experience. I even got > to meet my mentor in person, and other community members too, and to make > my first steps in bioinformatics. I even gave a small presentation at the > EU-codefest. What a summer it was! > > Thanks to everybody who made it possible: Google, Open Bioinformatics > Foundation and my mentor Pjotr Prins. > > -- > Marjan > > _______________________________________________ > 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 Wed Aug 22 04:16:13 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 22 Aug 2012 04:16:13 +0000 Subject: [BioRuby] GSoC final report In-Reply-To: <20120820095559.GB2453@thebird.nl> References: <20120820095559.GB2453@thebird.nl> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF33B73325@CHIMBX5.ad.uillinois.edu> Wholeheartedly agree. Congrats Artem on a job well done! chris On Aug 20, 2012, at 4:55 AM, Pjotr Prins wrote: > Thank you Artem, > > Great job. > > Pj. > > On Mon, Aug 20, 2012 at 01:47:18PM +0400, Artem Tarasov wrote: >> Hi all, >> >> here's a wrap-up of what was added/fixed in sambamba and Ruby bindings >> during the last couple of weeks: >> http://lomereiter.wordpress.com/2012/08/20/gsoc-weekly-report-12/ >> >> * Tools don't require input files to be seekable anymore, allowing to work >> with e.g. /dev/stdin and /dev/stdout >> * I've added an option of MessagePack output, that drastically improved >> speed of bindings (2-4x speedup depending on configuration) >> * The gem is on Travis CI now, passing tests on MRI 1.9.2/1.9.3. (JRuby >> also works, but on Travis there're problems with popen, same as with >> BioRuby) >> * The tool 'sambamba_filter' is now available on Galaxy Tool Shed. >> >> >> It's been a great summer. Thank you OBF/BioRuby folks :) >> >> >> -- >> Artem >> _______________________________________________ >> 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 georgkam at gmail.com Wed Aug 22 05:54:46 2012 From: georgkam at gmail.com (George Githinji) Date: Wed, 22 Aug 2012 08:54:46 +0300 Subject: [BioRuby] BioRuby 1.4.3 released In-Reply-To: <201208211644.q7LGiVsb026407@portal.open-bio.org> References: <201208211644.q7LGiVsb026407@portal.open-bio.org> Message-ID: Hi Thank you for all the bug fixes and the hard work. On Tue, Aug 21, 2012 at 7:37 PM, Naohisa GOTO wrote: > Hi, all, > > We are pleased to announce the release of BioRuby 1.4.3. > This new release fixes bugs existed in 1.4.2 and improves > portability on JRuby and Rubinius. > > Tar.gz file: http://bioruby.org/archive/bioruby-1.4.3.tar.gz > Gem file: http://bioruby.org/archive/gems/bio-1.4.3.gem > > We also put RubyGems pacakge at RubyGems.org and RubyForge (*). > (* Files on RubyForge will soon be available.) > > You can easily install by using RubyGems. First, check the > version number by using search command: > % gem search --remote bio > and find ?bio (1.4.3)? in the list. Then, > % sudo gem install bio > > Here is a brief summary of changes. > > * Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics > for storing a graphics element. > * Many failures and errors running on JRuby and Rubinius are resolved. > * Strange behavior related with ?circular require? is fixed. > * Fixed: Genomenet remote BLAST does not work. > * Fixed: Bio::NucleicAcid.to_re(?s?) typo. > * Fixed: Bio::EMBL#os raises RuntimeError. > * Fixed: bin/bioruby: Failed to save object with error message > "can?t convert Symbol into String" on Ruby 1.9. > > In addition, many changes have been made, including incompatible > changes. For more information, see RELEASE_NOTES.rdoc and > ChangeLog. > > Acknowledgments: Thanks to all persons reporting issues and/or > submitting patches. > > Hope you enjoy. > > P.S. We are having trouble when updating http://bioruby.org/ > and http://bioruby.open-bio.org/ webpages now, possibly because > of file/directory permissions in open-bio.org server. > > -- > Naohisa Goto > ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From lomereiter at gmail.com Wed Aug 22 06:42:12 2012 From: lomereiter at gmail.com (Artem Tarasov) Date: Wed, 22 Aug 2012 10:42:12 +0400 Subject: [BioRuby] [GSoC] Final GSoC report In-Reply-To: References: Message-ID: Hi, Unfortunately, the problem is on the side of D. PyD wiki ( https://bitbucket.org/ariovistus/pyd/wiki/Home) says that "extension libraries are nominally working with LDC (FE 2.060 or later); however, druntime currently limits what can be done here". However, this issue has become quite popular in last months, see e.g. this thread: http://forum.dlang.org/thread/mailman.1330.1345434177.31962.digitalmars-d at puremagic.com ? so maybe this'll get fixed soon. -- Artem On Wed, Aug 22, 2012 at 4:55 AM, Mic wrote: > Hi, > Python is able to connect to D with help of http://pyd.dsource.org/ . > > Maybe it would be something for Biopython > > Cheers, > Mic > > On Wed, Aug 22, 2012 at 5:11 AM, Marjan Povolni >wrote: > > > http://blog.mpthecoder.com/post/29910330225/final-gsoc-report > > > > *Summary* > > > > Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the > end > > of the summer. At least in GSoC terms. Should I say end of the project? I > > don?t think so. The tools can still be improved, and the Ruby bindings > > should follow. > > > > The major changes since the last release include the following: > > > > - filtering functionality has been moved to a separate utility: > > gff3-filter, along with a new language for specifying filtering > > expressions, > > - conversion to table format of selected fields has been moved to a > > separate utility: gff3-select. However, the ?select option is still > > part of > > gff3-filter, > > - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA > files > > for CDS and mRNA records and features, > > - man pages for utilities. > > > > ** > > The original idea was to create a GFF3/GTF parser in D and Ruby bindings. > > The Ruby bindings part didn?t work out because there is still no support > > for D shared libraries in Linux, but instead there are now a few useful > > command-line tools for processing GFF3 which can be used without > > programming knowledge. > > > > To me, the summer was fun, challenging, and a great experience. I even > got > > to meet my mentor in person, and other community members too, and to make > > my first steps in bioinformatics. I even gave a small presentation at the > > EU-codefest. What a summer it was! > > > > Thanks to everybody who made it possible: Google, Open Bioinformatics > > Foundation and my mentor Pjotr Prins. > > > > -- > > Marjan > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc > From francesco.strozzi at gmail.com Wed Aug 22 07:33:49 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Wed, 22 Aug 2012 09:33:49 +0200 Subject: [BioRuby] Bio-MAF 1.0.1 In-Reply-To: <20120821230126.GA22019@bartonh-mbp-01.mcd31065.det.wayport.net> References: <20120821214753.GB10348@thebird.nl> <20120821230126.GA22019@bartonh-mbp-01.mcd31065.det.wayport.net> Message-ID: Artem, Marjan, Clayton, you all did a great job, it was a pleasure to follow your progresses as a co-mentor and clearly you achieved all the goals for your projects. Your tools are already on my personal list and will be used in production in the next months on our facility here in Italy. Thanks for all the hard work and I hope you will stay in contact and contribute again with the community and the BioRuby people! Francesco On Wed, Aug 22, 2012 at 1:01 AM, Michael Barton wrote: > Yes, great work by both of you. I've enjoyed reading your blog posts and it has > great to see two bioinformaticians developing. Perhaps this may be obvious, I > think it is worth reiterating though: be sure to highlight this work when > applying for future positions. This is a great addition to your resume/CV. > > Thanks also to the BioRuby members who have committed their time to organising > and mentoring during this GSOC. > > Mike > > On Tue, Aug 21, 2012 at 11:47:53PM +0200, Pjotr Prins wrote: > >> Thank you Marjan and Clayton. It was our pleasure. >> >> Pj. >> >> On Tue, Aug 21, 2012 at 12:35:21PM -0700, Clayton Wheeler wrote: >> >> > Hi all, >> > >> > I've released bio-maf 1.0.1 and written a final GSoC blog post about >> > it: >> > >> > http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ >> > >> > This release should be substantially more robust, with solid and >> > reasonably-performing BGZF support, better CLI tools, and various >> > robustness, compatibility, and memory-footprint improvements. >> > >> > (I've also developed a Galaxy integration for the maf_tile tool; >> > unlike the existing Galaxy MAF tools, this is capable of filling >> > in gaps with a FASTA reference sequence, and concatenating >> > the alignment output from several exons specified in a BED >> > file. It's not quite all packaged up with the toolshed facility >> > yet, but I should be able to wrap that up shortly. Sneak preview: >> > https://gist.github.com/3418576) >> > >> > It's been a pleasure working with all of you, and I'm glad I've >> > been able to deliver something useful. Pjotr, Raoul, Francesco, >> > thanks for your help and advice this summer! Marjan, Artem, you >> > guys did excellent work and gave me some great suggestions in the >> > code reviews. And, of course, thanks to Google for organizing and >> > funding this! >> > >> > -- Clayton Wheeler cswh at umich.edu >> > ____________________________________________________________________ >> > 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 > > _______________________________________________ > 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 Aug 22 10:43:52 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 22 Aug 2012 12:43:52 +0200 Subject: [BioRuby] [GSoC] Final GSoC report In-Reply-To: References: Message-ID: <20120822104352.GA11847@thebird.nl> Yes, linking to D from an interpreted language is not hard, basically it is the same calling convention as that of C. So a D shared library looks the same as a C shared library to the calling code - all existing foreign function interfaces (FFI) work. That is the good news. The bad news, as Artem points out, is that there is a problem in the D garbage collector. Items get collected, which should not. This will be fixed sooner or later. The commitment is there, and it is moving up the priority list. For us it did not matter, as the parsers and tools happily run on their own using a command line interface, without much overhead. One advantage, from my perspective, is that we are not tied to Ruby, at this point, and the tools can be hosted in Galaxy. Another advantage, perhaps, is that we have not been side-tracked in providing rich library interfaces. That appeals to my purist side. Writing FFI bindings later is not a problem. Pj. On Wed, Aug 22, 2012 at 10:42:12AM +0400, Artem Tarasov wrote: > Hi, > > Unfortunately, the problem is on the side of D. PyD wiki ( > https://bitbucket.org/ariovistus/pyd/wiki/Home) says that "extension > libraries are nominally working with LDC (FE 2.060 or later); however, > druntime currently limits what can be done here". > > However, this issue has become quite popular in last months, see e.g. this > thread: > http://forum.dlang.org/thread/mailman.1330.1345434177.31962.digitalmars-d at puremagic.com > ? > so maybe this'll get fixed soon. > > -- > Artem > > On Wed, Aug 22, 2012 at 4:55 AM, Mic wrote: > > > Hi, > > Python is able to connect to D with help of http://pyd.dsource.org/ . > > > > Maybe it would be something for Biopython > > > > Cheers, > > Mic > > > > On Wed, Aug 22, 2012 at 5:11 AM, Marjan Povolni > >wrote: > > > > > http://blog.mpthecoder.com/post/29910330225/final-gsoc-report > > > > > > *Summary* > > > > > > Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the > > end > > > of the summer. At least in GSoC terms. Should I say end of the project? I > > > don?t think so. The tools can still be improved, and the Ruby bindings > > > should follow. > > > > > > The major changes since the last release include the following: > > > > > > - filtering functionality has been moved to a separate utility: > > > gff3-filter, along with a new language for specifying filtering > > > expressions, > > > - conversion to table format of selected fields has been moved to a > > > separate utility: gff3-select. However, the ?select option is still > > > part of > > > gff3-filter, > > > - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA > > files > > > for CDS and mRNA records and features, > > > - man pages for utilities. > > > > > > ** > > > The original idea was to create a GFF3/GTF parser in D and Ruby bindings. > > > The Ruby bindings part didn?t work out because there is still no support > > > for D shared libraries in Linux, but instead there are now a few useful > > > command-line tools for processing GFF3 which can be used without > > > programming knowledge. > > > > > > To me, the summer was fun, challenging, and a great experience. I even > > got > > > to meet my mentor in person, and other community members too, and to make > > > my first steps in bioinformatics. I even gave a small presentation at the > > > EU-codefest. What a summer it was! > > > > > > Thanks to everybody who made it possible: Google, Open Bioinformatics > > > Foundation and my mentor Pjotr Prins. > > > > > > -- > > > Marjan > > > > > > _______________________________________________ > > > BioRuby Project - http://www.bioruby.org/ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > _______________________________________________ > > GSoC mailing list > > GSoC at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/gsoc > > > > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc From p.j.a.cock at googlemail.com Wed Aug 22 11:10:56 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 22 Aug 2012 12:10:56 +0100 Subject: [BioRuby] [GSoC] Final GSoC report In-Reply-To: <20120822104352.GA11847@thebird.nl> References: <20120822104352.GA11847@thebird.nl> Message-ID: On Wed, Aug 22, 2012 at 11:43 AM, Pjotr Prins wrote: > Yes, linking to D from an interpreted language is not hard, basically > it is the same calling convention as that of C. So a D shared library > looks the same as a C shared library to the calling code - all > existing foreign function interfaces (FFI) work. That is the good > news. How do things stand from a cross-platform perspective? i.e. When might this be doable on Linux, Mac OS X, and Windows? (and other Unix like platforms of potential interest) > The bad news, as Artem points out, is that there is a problem in the > D garbage collector. Items get collected, which should not. This will > be fixed sooner or later. The commitment is there, and it is moving > up the priority list. Is there a D issue/bug tracker for this? Thanks, Peter From cjfields at illinois.edu Wed Aug 22 12:46:37 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 22 Aug 2012 12:46:37 +0000 Subject: [BioRuby] Bio-MAF 1.0.1 In-Reply-To: References: <20120821214753.GB10348@thebird.nl> <20120821230126.GA22019@bartonh-mbp-01.mcd31065.det.wayport.net> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF33B73926@CHIMBX5.ad.uillinois.edu> I agree. I think this is likely the most successful of the GSoC runs I've seen. It definitely sets the bar high for the future. chris On Aug 22, 2012, at 2:33 AM, Francesco Strozzi wrote: > Artem, Marjan, Clayton, > > you all did a great job, it was a pleasure to follow your progresses > as a co-mentor and clearly you achieved all the goals for your > projects. Your tools are already on my personal list and will be used > in production in the next months on our facility here in Italy. > > Thanks for all the hard work and I hope you will stay in contact and > contribute again with the community and the BioRuby people! > > Francesco > > On Wed, Aug 22, 2012 at 1:01 AM, Michael Barton > wrote: >> Yes, great work by both of you. I've enjoyed reading your blog posts and it has >> great to see two bioinformaticians developing. Perhaps this may be obvious, I >> think it is worth reiterating though: be sure to highlight this work when >> applying for future positions. This is a great addition to your resume/CV. >> >> Thanks also to the BioRuby members who have committed their time to organising >> and mentoring during this GSOC. >> >> Mike >> >> On Tue, Aug 21, 2012 at 11:47:53PM +0200, Pjotr Prins wrote: >> >>> Thank you Marjan and Clayton. It was our pleasure. >>> >>> Pj. >>> >>> On Tue, Aug 21, 2012 at 12:35:21PM -0700, Clayton Wheeler wrote: >>> >>>> Hi all, >>>> >>>> I've released bio-maf 1.0.1 and written a final GSoC blog post about >>>> it: >>>> >>>> http://csw.github.com/bioruby-maf/blog/2012/08/21/bio-maf_1.0.1/ >>>> >>>> This release should be substantially more robust, with solid and >>>> reasonably-performing BGZF support, better CLI tools, and various >>>> robustness, compatibility, and memory-footprint improvements. >>>> >>>> (I've also developed a Galaxy integration for the maf_tile tool; >>>> unlike the existing Galaxy MAF tools, this is capable of filling >>>> in gaps with a FASTA reference sequence, and concatenating >>>> the alignment output from several exons specified in a BED >>>> file. It's not quite all packaged up with the toolshed facility >>>> yet, but I should be able to wrap that up shortly. Sneak preview: >>>> https://gist.github.com/3418576) >>>> >>>> It's been a pleasure working with all of you, and I'm glad I've >>>> been able to deliver something useful. Pjotr, Raoul, Francesco, >>>> thanks for your help and advice this summer! Marjan, Artem, you >>>> guys did excellent work and gave me some great suggestions in the >>>> code reviews. And, of course, thanks to Google for organizing and >>>> funding this! >>>> >>>> -- Clayton Wheeler cswh at umich.edu >>>> ____________________________________________________________________ >>>> 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 >> >> _______________________________________________ >> 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