[BioRuby] samtools-ruby

Thu Feb 3 11:56:00 UTC 2011

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.