[BioRuby] samtools-ruby

Raoul Bonnal bonnalraoul at ingm.it
Fri Feb 4 10:33:05 UTC 2011 

Thanks, 
please not that I found a problem using TopHat with samtools 0.1.12a I sent a mail to TopHat's developer but I didn't receive any answer yet.

this is the original message : 

I'm Raoul a bioinformaticians, I'll start working on illumina data set in few days; in the mean time my group is doing tests.
So, I have installed all the software, latest releases and today running my first alignment with tophat I got this error:
[Fri Jan 28 10:43:20 2011] Checking for Samtools
Traceback (most recent call last):
File "/usr/local/bin/tophat", line 2223, in ?
  sys.exit(main())
File "/usr/local/bin/tophat", line 2136, in main
  check_samtools()
File "/usr/local/bin/tophat", line 877, in check_samtools
  samtools_version = get_samtools_version()
File "/usr/local/bin/tophat", line 864, in get_samtools_version
  samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')]
ValueError: invalid literal for int(): 12a


My samtools is 
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.12a (r862)

so i fixed the line #864 with 
          import re
          samtools_version = [int(re.sub('[a-z]','',x.split('-')[0])) for x in version_val.split('.')]

I know that it's quite ugly solution but .... I'm a ruby man :-) and I want to let you know that we, bioruby dev team, are putting a lot of effort to support your suite.

Cheers.
On 04/feb/2011, at 08.56, Michal wrote:

> Please find attached the libbam.so.1 of samtools-0.1.12a.
> 
> 
> On 02/03/2011 09:56 PM, Raoul Bonnal wrote:
>> Thanks Tomoaki
>> I missed the linux lib sorry, could you send me that library I'll add it to the repo.
>> so.1 fixed
>> 
>> On 03/feb/2011, at 11.10, Tomoaki NISHIYAMA wrote:
>> 
>>> Hi,
>>> 
>>> As it says.
>>> 
>>>> Run `bundle install` to install missing gems
>>> 
>>> $ bundle install
>>> 
>>> will install all other required gems.
>>> 
>>> The next thing to do is for the error:
>>> 
>>> /home/tomoaki/ruby192p136/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in `block in ffi_lib': Could not open library '/home/tomoaki/bioruby-samtools/lib/bio/db/sam/external/libbam.a':
>>> 
>>> Its natural that a dynamic library should be made for the purpose as is in Mac OS X.
>>> 
>>> $ make dylib
>>> in the latest samtools and copy libbam.so.1 to bioruby-samtools/lib/bio/db/sam/external/
>>> 
>>> 
>>> ------------CUT
>>> diff --git a/lib/bio/db/sam/external/libbam.a b/lib/bio/db/sam/external/libbam.a
>>> index 0f231ef..aa1b225 100644
>>> Binary files a/lib/bio/db/sam/external/libbam.a and b/lib/bio/db/sam/external/libbam.a differ
>>> diff --git a/lib/bio/db/sam/library.rb b/lib/bio/db/sam/library.rb
>>> index bb78515..e9f8b6e 100644
>>> --- a/lib/bio/db/sam/library.rb
>>> +++ b/lib/bio/db/sam/library.rb
>>> @@ -9,7 +9,7 @@ module Bio
>>>           #TODO refactor this piece of code in all the files
>>>           lib_os = case RUBY_PLATFORM
>>>           when /linux/
>>> -            'a'
>>> +            'so.1'
>>>           when /darwin/
>>>             'dylib'
>>>           when /windows/
>>> @@ -22,4 +22,4 @@ module Bio
>>>       end #Library
>>>     end #Sam
>>>   end #DB
>>> -end #Bio
>>> \ No newline at end of file
>>> +end #Bio
>>> ------------CUT
>>> 
>>> Then finally reached this state
>>> 
>>> $ ~/ruby192p136/bin/rake
>>> (in /home/tomoaki/bioruby-samtools)
>>> /home/tomoaki/ruby192p136/bin/ruby -I"lib:lib:test" "/home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader.rb" "test/test_bio-samtools.rb"
>>> Loaded suite /home/tomoaki/ruby192p136/lib/ruby/1.9.1/rake/rake_test_loader
>>> Started
>>> F
>>> Finished in 0.000321 seconds.
>>> 
>>>  1) Failure:
>>> test: BioSamtools should probably rename this file and start testing for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]:
>>> hey buddy, you should probably rename this file and start testing for real
>>> 
>>> Loading seems ok.
>>> I'm not sure if this is bad or ok.
>>> 
>>> Best regards
>>> -- 
>>> Tomoaki NISHIYAMA
>>> 
>>> Advanced Science Research Center,
>>> Kanazawa University,
>>> 13-1 Takara-machi,
>>> Kanazawa, 920-0934, Japan
>>> 
>>> 
>>> On 2011/02/03, at 17:16, Michal wrote:
>>> 
>>>> Dear Raoul,
>>>> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way:
>>>> $ tar xvfz ruby-1.9.2-p136.tar.gz
>>>> $ cd ruby-1.9.2-p136/
>>>> $ ./configure --prefix=/home/mictadlo/apps/ruby
>>>> $ make
>>>> $ make install
>>>> $ vim ~/.bashrc
>>>>  export APPS=/home/mictadlo/apps
>>>>  export RUBY_HOME=$APPS/ruby
>>>>  export LD_LIBRARY_PATH=/RUBY_HOME/lib
>>>>  PATH=$RUBY_HOME/bin:$PATH
>>>> $ . ~/.bashrc
>>>> $ ruby -v
>>>>  ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux]
>>>> 
>>>> $ gem install ffi
>>>> Building native extensions.  This could take a while...
>>>> Successfully installed ffi-1.0.5
>>>> 1 gem installed
>>>> Installing ri documentation for ffi-1.0.5...
>>>> Installing RDoc documentation for ffi-1.0.5...
>>>> 
>>>> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git
>>>> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/
>>>> remote: Counting objects: 92, done.
>>>> remote: Compressing objects: 100% (84/84), done.
>>>> remote: Total 92 (delta 21), reused 0 (delta 0)
>>>> Unpacking objects: 100% (92/92), done.
>>>> 
>>>> ~/Downloads/git/bioruby-samtools$ rake test
>>>> (in /home/mictadlo/Downloads/git/bioruby-samtools)
>>>> rake aborted!
>>>> no such file to load -- bundler
>>>> <internal:lib/rubygems/custom_require>:29:in `require'
>>>> <internal:lib/rubygems/custom_require>:29:in `require'
>>>> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `<top (required)>'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run'
>>>> /home/mictadlo/apps/ruby/bin/rake:31:in `<main>'
>>>> 
>>>> What did I wrong?
>>>> 
>>>> Thank you in advance.
>>>> 
>>>> Michal
>>>> 
>>>> On 01/31/2011 08:11 PM, Raoul Bonnal wrote:
>>>>> Dear Michal,
>>>>> please check this out:
>>>>> 
>>>>> https://github.com/helios/bioruby-samtools
>>>>> 
>>>>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows.
>>>>> I need to test the linux library because I'm developing under osx.
>>>>> If the libbam.a is wrong please give me the right one and I'll add it to the repo.
>>>>> Also note that the library has been compiled for 64bit.
>>>>> 
>>>>> Ciao!
>>>>> 
>>>>> On 30/gen/2011, at 12.42, Michal wrote:
>>>>> 
>>>>>> Hi,
>>>>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response.
>>>>>> 
>>>>>> What did I wrong?
>>>>>> 
>>>>>> Michal
>>>>>> _______________________________________________
>>>>>> BioRuby Project - http://www.bioruby.org/
>>>>>> BioRuby mailing list
>>>>>> BioRuby at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>>>> --
>>>>> R.J.P.B.
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>> _______________________________________________
>>>> BioRuby Project - http://www.bioruby.org/
>>>> BioRuby mailing list
>>>> BioRuby at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>>> 
>> --
>> R.J.P.B.
>> 
>> 
>> 
>> 
>> 
> 
> <libbam.so.1>

--
R.J.P.B.

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