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Efraim Flashner c0c6263202 gn: Fix ratspub python error. преди 1 година
gn gn: Fix ratspub python error. преди 1 година
.gitignore Ignore editor temporary files преди 3 години
LICENSE LICENSE преди 6 години Links преди 1 година
arrayfire-lapack-detection.patch gn: Fix building arrayfire. преди 2 години
arrayfire-newer-boost-compute.patch gn: Fix building arrayfire. преди 2 години
delly-use-system-libraries.patch Add delly. преди 5 години
gnulib-gets.patch gn: Add octave@3.4.3. преди 2 години
htslib-add-cram_to_bam.patch Cleaner patch file. преди 5 години
keras-auc-optimizer.patch gn: Fix ratspub python error. преди 1 година
ldc-disable-tests2.patch LDC преди 3 години
ldc-druntime-finiTLSRanges.patch Patching Druntime for sambamba преди 4 години
mongodb-add-version-file.patch Add mongodb. преди 5 години
octave-nested-class.patch gn: Add octave@3.4.3. преди 2 години
plink-ng-Makefile-zlib.patch plink2 installs with patched Makefile преди 5 години
python2-htmlgen-Applied-Deb-patch.patch python2-htmlgen patches преди 5 години
python2-htmlgen-Fix-test-for-random.patch Fix name of patch преди 5 години


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




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+