guix-bioinformatics

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

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

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

git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i environment-modules

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

python2-numarray 1.5.2

Install the module environment with

git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i python2-numarray

Common Workflow Language (CWL)

Install the common workflow language tool cwltool with

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

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+