選択できるのは25トピックまでです。 トピックは、先頭が英数字で、英数字とダッシュ('-')を使用した35文字以内のものにしてください。
Bonface Munyoki b0c38d1513
gn: genenetwork2: Add pillow as one of the propagated-inputs
7時間前
gn gn: genenetwork2: Add pillow as one of the propagated-inputs 7時間前
.gitignore Ignore editor temporary files 2年前
.guix-channel gn: Use the guix-past channel. 1ヶ月前
LICENSE LICENSE 4年前
README.org gn: Use the guix-past channel. 1ヶ月前
arrayfire-lapack-detection.patch gn: Fix building arrayfire. 1年前
arrayfire-newer-boost-compute.patch gn: Fix building arrayfire. 1年前
delly-use-system-libraries.patch Add delly. 4年前
gnulib-gets.patch gn: Add octave@3.4.3. 1年前
htslib-add-cram_to_bam.patch Cleaner patch file. 4年前
keras-auc-optimizer.patch gn: Fix ratspub python error. 3ヶ月前
ldc-disable-tests2.patch LDC 2年前
ldc-druntime-finiTLSRanges.patch Patching Druntime for sambamba 3年前
mongodb-add-version-file.patch Add mongodb. 4年前
octave-nested-class.patch gn: Add octave@3.4.3. 1年前
plink-ng-Makefile-zlib.patch plink2 installs with patched Makefile 4年前
python2-htmlgen-Applied-Deb-patch.patch python2-htmlgen patches 4年前
python2-htmlgen-Fix-test-for-random.patch Fix name of patch 4年前

README.org

guix-bioinformatics

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

  1. https://github.com/BIMSBbioinfo

  2. https://github.com/UMCUGenetics/guix-additions

  3. https://github.com/ekg/guix-genomics

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:

    (cons*
      (channel
        (name 'gn-bioinformatics)
        (url "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git")
        (branch "master"))
      %default-channels)

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 https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git
    git clone https://gitlab.inria.fr/guix-hpc/guix-past.git
    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
      VERSION=3.2.10
      DATE=2012-12-21

Common Workflow Language (CWL)

Install the common workflow language tool cwltool with

    guix pull
    guix package -i python2-cwltool

    cwtool --version
      1.0.20150916041152

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+