| Please visit our ***NEW*** OBF/BOSC website: https://www.open-bio.org/ |
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Difference between revisions of "Bio-packaging"
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=== GNU Guix === | === GNU Guix === | ||
| − | [https://www.gnu.org/software/guix GNU guix] is a package manager for the Gnu/Linux operating system. Bioinformatics packages are constructed [http://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/bioinformatics.scm here]. | + | [https://www.gnu.org/software/guix GNU guix] is a package manager for the Gnu/Linux operating system. Bioinformatics packages are constructed [http://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/bioinformatics.scm here]. GNU Guix can be run inside any Linux distribution (it is distribution agnostic because all software installs under /gnu). |
== Language based packaging systems == | == Language based packaging systems == | ||
Revision as of 17:32, 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.
Contents
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).
Language based packaging systems
Ruby biogems
- Biogems: http://biogems.info/
Python packages
Perl CPAN
R CRAN
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
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.
