guix-bioinformatics

Bioinformatics packages for GNU Guix that are used in http://genenetwork.org/. See Guix Notes for installing and hacking GNU Guix.

To easily use the packages from this repo, simply add it to your channels list:

(cons*
  (channel
    (name 'gn-bioinformatics)
    (url "https://gitlab.com/genenetwork/guix-bioinformatics")
    (branch "master"))
  %default-channels)

and run guix pull like normal to update your software. This is the recommended way to use the software from this repository and the code snippets in this README assume you have done so.

If you want to make changes to the packages in this repo then simply set the GUIX_PACKAGE_PATH to point to the root of this directory before running Guix. E.g.

git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -A cwl

or using a checked out Guix repo with

env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -A cwl

Some (or most) of these package definitions should make it upstream into the GNU Guix repository when tested and stable.

Slurm and munge

Install slurm with

guix pull
guix package -i slurm-llnl

~/.guix-profile/sbin/slurmd -C -D
  ClusterName=(null) NodeName=selinunte CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=2 ThreadsPerCore=2 RealMemory=7890 TmpDisk=29909

Module system

Install the module environment with

guix pull
guix package -i environment-modules

modulecmd --version
  VERSION=3.2.10
  DATE=2012-12-21

python2-numarray 1.5.2

Install python2-numarray package with

guix pull
guix package -i python2-numarray

Common Workflow Language (CWL)

Install the common workflow language tool cwltool with

guix pull
guix package -i python2-cwltool

cwtool --version
  1.0.20150916041152

Packages moved from here to main line GNU Guix

LLVM D compiler

The LLVM D compiler was added to GNU Guix main stream!

guix package -i ldc

Elixir and Erlang

Both languages have gone in to main line Guix:

guix package -i elixir
guix package -i erlang

R/qtl

R-qtl is now part of main stream GNU Guix:

guix package -i r-qtl r

Development tips

Override individual packages

The cheerful way of overriding a version of a package:

(use-modules (guix) (gnu packages emacs))

(package
  (inherit emacs)
  (name "emacs-snapshot")
  (source "/path/to/some-file-or-directory.tar.gz"))

and then run:

guix package --install-from-file=that-file.scm

LICENSE

These package descriptions (so-called Guix expressions) are distributed by the same license as GNU Guix, i.e. GPL3+