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Difference between revisions of "Bio-packaging"
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| − | 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 | + | 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) |
| + | [http://lists.open-bio.org/mailman/listinfo/bio-packaging bio-packaging mailing list]. | ||
| + | |||
| + | On the mailing list 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 === | |
| + | |||
| + | [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). There may be OSX/Cygwin support in the future, but currently the targets are Linux and Hurd. | ||
| + | |||
| + | === GNU Guix for bioinformatics === | ||
| + | |||
| + | For Bio-packaging we created a [https://github.com/genenetwork/guix/wiki/GNU-Guix-for-bioinformatics GNU Guix edition for bioinformatics]. See also GNU Guix [https://www.gnu.org/software/guix/manual/guix.html documentation] and Pjotr Prins' [https://github.com/pjotrp/guix-notes guix-notes] and Malcolm Cook's [https://github.com/malcook/sce manual] | ||
| + | |||
| + | == Language based packaging systems == | ||
| + | |||
| + | === Ruby biogems === | ||
| + | |||
| + | * [http://biogems.info/ 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 === | ||
| + | |||
| + | [https://www.debian.org/devel/debian-med/ Debian Med] contains a wide range of bioinformatics software packages target at Debian Linux and derivatives. See also the [https://wiki.debian.org/ReproducibleBuilds Debian reproducible builds] initiative. | ||
| + | |||
| + | === CloudBiolinux === | ||
| + | |||
| + | [http://cloudbiolinux.org CloudBioLinux] offers genome analysis resources for cloud computing platforms such as Amazon EC2. The source code can be found [https://github.com/chapmanb/cloudbiolinux here]. CloudBiolinux uses a combination of Debian/Ubuntu packages with linuxbrew and self-compiled software. | ||
| + | |||
| + | === Galaxy === | ||
| + | === Docker === | ||
Latest revision as of 15:55, 11 June 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.
On the mailing list 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). There may be OSX/Cygwin support in the future, but currently the targets are Linux and Hurd.
GNU Guix for bioinformatics
For Bio-packaging we created a GNU Guix edition for bioinformatics. See also GNU Guix documentation and Pjotr Prins' guix-notes and Malcolm Cook's manual
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
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.
