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guix-bioinformatics

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

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

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

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

Install 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

Install R/qtl

git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i r-qtl r
R
  library(qtl)

LICENSE

These package descriptions are distributed by the same license as GNU Guix, i.e. GPL3+