Difference between revisions of "Bio-packaging"

Revision as of 21:38, 30 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. GNU Guix can be run inside any Linux distribution (it is distribution agnostic because all software installs under /gnu). There may be OSX/Cygwin support in the future, but currently the targets are Linux and Hurd. See also GNU Guix documentation and Pjotr's guix-notes

Language based packaging systems

Ruby biogems

• biogems are Ruby packages (gems) that can install globally or in HOME. To make sure gems do not conflict with multiple Ruby versions it is possible to use RVM, rbenv and/or GNU Guix.

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 bioinformatics software packages target at Debian Linux and derivatives. See also the Debian reproducible builds initiative.

CloudBiolinux

CloudBioLinux offers genome analysis resources for cloud computing platforms such as Amazon EC2. The source code can be found here. CloudBiolinux uses a combination of Debian/Ubuntu packages with linuxbrew and self-compiled software.

Galaxy

Docker