[BioRuby] samtools-ruby

Thu Feb 3 10:10:28 UTC 2011

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
>


