[BioRuby] samtools-ruby

[Michal]

Hi Philipp,
Bundler fix one problem, but I have got a new one:

$ gem install bundler
Successfully installed bundler-1.0.10
1 gem installed
Installing ri documentation for bundler-1.0.10...
Installing RDoc documentation for bundler-1.0.10...

~/Downloads/git/bioruby-samtools$ rake test
(in /home/uqmlore1/Downloads/git/bioruby-samtools)
Could not find bio-1.4.1 in any of the sources
Run `bundle install` to install missing gems

$ irb
irb(main):001:0> require "bio"
=> true
irb(main):002:0> exit

$ bioruby
Loading config (/home/uqmlore1/.bioruby/shell/session/config) ... done
Loading object (/home/uqmlore1/.bioruby/shell/session/object) ... Error: 
Failed to load (/home/uqmlore1/.bioruby/shell/session/object) : marshal 
data too short
done

. . . B i o R u b y   i n   t h e   s h e l l . . .

   Version : BioRuby 1.4.1 / Ruby 1.9.2


Thank you in advance.

Michal


On 02/03/2011 07:03 PM, Philipp Comans wrote:
> Try gem install bundler
>
> Am 03.02.2011 um 09:16 schrieb Michal<mictadlo at gmail.com>:
>
>> 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