[BioRuby] samtools-ruby

[Michal]

Dear Raoul,
I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in 
the following way:
  $ tar xvfz ruby-1.9.2-p136.tar.gz
  $ cd ruby-1.9.2-p136/
  $ ./configure --prefix=/home/mictadlo/apps/ruby
  $ make
  $ make install
  $ vim ~/.bashrc
   export APPS=/home/mictadlo/apps
   export RUBY_HOME=$APPS/ruby
   export LD_LIBRARY_PATH=/RUBY_HOME/lib
   PATH=$RUBY_HOME/bin:$PATH
  $ . ~/.bashrc
  $ ruby -v
   ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux]

$ gem install ffi
Building native extensions.  This could take a while...
Successfully installed ffi-1.0.5
1 gem installed
Installing ri documentation for ffi-1.0.5...
Installing RDoc documentation for ffi-1.0.5...

~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git
Initialized empty Git repository in 
/home/mictadlo/Downloads/git/bioruby-samtools/.git/
remote: Counting objects: 92, done.
remote: Compressing objects: 100% (84/84), done.
remote: Total 92 (delta 21), reused 0 (delta 0)
Unpacking objects: 100% (92/92), done.

~/Downloads/git/bioruby-samtools$ rake test
(in /home/mictadlo/Downloads/git/bioruby-samtools)
rake aborted!
no such file to load -- bundler
<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.
>
>
>
>
>