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pjotrp 9e1e668e4f Added python testing framework packages pirms 2 dienas
gn Added python testing framework packages pirms 2 dienas
.gitignore Ignore editor temporary files pirms 2 gadiem
.guix-channel gn: Use the guix-past channel. pirms 2 mēnešiem
LICENSE LICENSE pirms 5 gadiem gn: Use the guix-past channel. pirms 2 mēnešiem
arrayfire-lapack-detection.patch gn: Fix building arrayfire. pirms 1 gada
arrayfire-newer-boost-compute.patch gn: Fix building arrayfire. pirms 1 gada
delly-use-system-libraries.patch Add delly. pirms 4 gadiem
gnulib-gets.patch gn: Add octave@3.4.3. pirms 1 gada
htslib-add-cram_to_bam.patch Cleaner patch file. pirms 4 gadiem
keras-auc-optimizer.patch gn: Fix ratspub python error. pirms 5 mēnešiem
ldc-disable-tests2.patch LDC pirms 2 gadiem
ldc-druntime-finiTLSRanges.patch Patching Druntime for sambamba pirms 3 gadiem
mongodb-add-version-file.patch Add mongodb. pirms 4 gadiem
octave-nested-class.patch gn: Add octave@3.4.3. pirms 1 gada
plink-ng-Makefile-zlib.patch plink2 installs with patched Makefile pirms 4 gadiem
python2-htmlgen-Applied-Deb-patch.patch python2-htmlgen patches pirms 4 gadiem
python2-htmlgen-Fix-test-for-random.patch Fix name of patch pirms 4 gadiem
vg-use-packaged-deps.patch Add vg pirms 4 nedēļām


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
    git clone
    export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/:$PWD/guix-past/modules
    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+