Difference between revisions of "Bio-packaging"

Revision as of 20:15, 29 May 2015

If you are in any way interested in software packaging and deployment for bioinformatics you can meet like-minded people on the Open Bioinformatics Foundation (OBF) bio-packaging mailing list at

   http://lists.open-bio.org/mailman/listinfo/bio-packaging

Here we discuss issues around packaging and deploying software: anything that concerns dependencies, multiple version support and/or reproducibility. The general idea is to come up with solutions we can share across environments and construct (shared) pipelines out of them.

Generic packaging systems

GNU Guix

GNU guix is a package manager for the Gnu/Linux operating system. Bioinformatics packages are constructed here.

Language based packaging systems

Ruby biogems

• Biogems: http://biogems.info/

Python packages

Perl CPAN

R CRAN

• http://cran.r-project.org/

Javascript

• node.js npm: https://www.npmjs.com
• javascript, bower: http://bower.io

Linux distributions and VMs

Debian Med

Debian Med contains a wide range of software packages target at Debian Linux and derivatives.

CloudBiolinux

Galaxy

Docker