You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
Pjotr Prins 21efb11c56 Genenetwork1 2 maanden geleden
gn Genenetwork1 2 maanden geleden
.gitignore Ignore editor temporary files 2 jaren geleden
LICENSE LICENSE 4 jaren geleden URL 6 maanden geleden
arrayfire-lapack-detection.patch gn: Fix building arrayfire. 1 jaar geleden
arrayfire-newer-boost-compute.patch gn: Fix building arrayfire. 1 jaar geleden
delly-use-system-libraries.patch Add delly. 4 jaren geleden
gnulib-gets.patch gn: Add octave@3.4.3. 1 jaar geleden
htslib-add-cram_to_bam.patch Cleaner patch file. 4 jaren geleden
keras-auc-optimizer.patch gn: Fix ratspub python error. 3 maanden geleden
ldc-disable-tests2.patch LDC 2 jaren geleden
ldc-druntime-finiTLSRanges.patch Patching Druntime for sambamba 3 jaren geleden
mongodb-add-version-file.patch Add mongodb. 4 jaren geleden
octave-nested-class.patch gn: Add octave@3.4.3. 1 jaar geleden
plink-ng-Makefile-zlib.patch plink2 installs with patched Makefile 4 jaren geleden
python2-htmlgen-Applied-Deb-patch.patch python2-htmlgen patches 4 jaren geleden
python2-htmlgen-Fix-test-for-random.patch Fix name of patch 4 jaren geleden


Bioinformatics packages for GNU Guix that are used in and some other places. See Guix notes for installing and hacking GNU Guix. Other channels of bioinformatics interest can be found at




Also see Guix notes for a list of channels.

To easily use the packages from this repo, simply add it to your `channels` list in ~/.config/guix/channels.scm as described here:

        (name 'gn-bioinformatics)
        (url "")
        (branch "master"))

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
    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

Common Workflow Language (CWL)

Install the common workflow language tool cwltool with

    guix pull
    guix package -i python2-cwltool

    cwtool --version

Development tips

Override individual packages

The cheerful way of overriding a version of a package:

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

      (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


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