[BioRuby] GNU Guix

[Pjotr Prins]

Hi everyone,

I have written about GNU Guix before and now it is time for an update.
With the release of 0.8.1 it is becoming rather good.

  https://news.ycombinator.com/item?id=8965257

Interestingly 

* LLVM support has gone in (and Guix being Guix you can have multiple versions)
* People are adding bioinformatics packages to Guix
* Great Python, R, Julia and Ruby support
* There are almost 100 python modules in there now(!)

The last is interesting. My take is that because Python's packaging
is such a mess they are now leapfrogging the competition (i.e. us
Ruby folks) with Guix ;)

I have been using GNU Guix daily over a year now and I love it. E.g.

  ruby -v
  ruby 2.1.5p273 (2014-11-13 revision 48405) [x86_64-linux]

  gem env

  RubyGems Environment:
  - RUBYGEMS VERSION: 2.2.2
  - RUBY VERSION: 2.1.5 (2014-11-13 patchlevel 273) [x86_64-linux]
  - INSTALLATION DIRECTORY: /home/pjotr/.gem/z1v7183grkhz33xnzr6bb1qwg2qn2s79-ruby-2.1.5/2.1.0
  - RUBY EXECUTABLE: /gnu/store/z1v7183grkhz33xnzr6bb1qwg2qn2s79-ruby-2.1.5/bin/ruby
  - EXECUTABLE DIRECTORY: /home/pjotr/.gem/z1v7183grkhz33xnzr6bb1qwg2qn2s79-ruby-2.1.5/2.1.0/bin
  - SPEC CACHE DIRECTORY: /home/pjotr/.gem/z1v7183grkhz33xnzr6bb1qwg2qn2s79-ruby-2.1.5/specs
  - RUBYGEMS PLATFORMS:
    - ruby
    - x86_64-linux
  - GEM PATHS:
     - /home/pjotr/.gem/z1v7183grkhz33xnzr6bb1qwg2qn2s79-ruby-2.1.5/2.1.0
  - GEM CONFIGURATION:
     - :update_sources => true
     - :verbose => true
     - :backtrace => false
     - :bulk_threshold => 1000
  - REMOTE SOURCES:
     - https://rubygems.org/
  - SHELL PATH:
     - /home/pjotr/.gem/z1v7183grkhz33xnzr6bb1qwg2qn2s79-ruby-2.1.5/2.1.0/bin/
     - /home/pjotr/.guix-profile/bin
     - /usr/bin
     - /bin
     - /usr/sbin
     - /sbin
     - /usr/local/bin

Just saying. Total separation of Ruby and gems. No more RVM mess or mixing with
Debian/Ubuntu installs.

If anyone is interested in *sane* software deployment with Ruby
and/or bioinformatics, I invite you to send us (or me) an E-mail. I'll
set up a mailing list for the purpose.

Pj.