guix-bioinformatics

IMPORTANT: this repository has moved to https://git.genenetwork.org/guix-bioinformatics/!

Bioinformatics packages for GNU Guix that are used in https://genenetwork.org/ 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:

(list (channel
       (name 'gn-bioinformatics)
       (url "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git")
       (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. In order to maintain stability, the guix-bioinformatics channel depends on a specific commit of upstream Guix. So, it is recommended to isolate use of the guix-bioinformatics channel in a separate guix pull profile. That is described here.

If you want to make changes to the packages in this repo you can 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

Common Workflow Language (CWL)

Note that CWL moved into Guix master!

Install the common workflow language tool cwltool from this repo with

    guix pull
    export PATH=$HOME/.config/guix/current/bin/guix:$PATH
    ~/guix-bioinformatics$ env GUIX_PACKAGE_PATH=.:../guix-past/modules/ ~/.config/guix/current/bin/guix package -i cwl-runner -p ~/opt/CWL

The following package will be installed:
   cwl-runner 1.0

The following derivations will be built:
   /gnu/store/ld59374zr45rbqanh7ccfi2wa4d5x4yl-cwl-runner-1.0.drv
   /gnu/store/86j15mxj5zp3k3sjimhqhb6zsj19azsf-python-schema-salad-7.0.20200811075006.drv
   /gnu/store/0q2ls0is3253r4gx6hs7kmvlcz412lh1-schema-salad-7.0.20200811075006.tar.gz.drv
   /gnu/store/myj1365ph687ynahjhg6zqslrmd6zpjq-cwltool-3.0.20201117141248.drv

source ~/opt/CWL/etc/profile
cwltool --version
  /gnu/store/50mncjcgc8vmq5dfrh0pb82avbzy8c4r-cwltool-3.0.20201117141248/bin/.cwltool-real 3.0

To run CWL definitions you can install tools in a Guix environment (avoiding Docker). Say you need mafft in a workflow

~/guix-bioinformatics$ env GUIX_PACKAGE_PATH=.:../guix-past/modules/ ~/.config/guix/current/bin/guix environment \
   guix --ad-hoc cwl-runner mafft

in the new shell you should be able to find both CWL and MAFFT:

ls $GUIX_ENVIRONMENT/bin/cwl*
/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/cwl-runner
/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/cwltool
ls $GUIX_ENVIRONMENT/bin/mafft
/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/mafft

The paths can be loaded into the shell with

source $GUIX_ENVIRONMENT/etc/profile

Module system

For those who think they need modules: install the module environment with

guix pull
guix package -i environment-modules

modulecmd --version
  VERSION=3.2.10
  DATE=2012-12-21

Note that GNU Guix supercedes module functionality!

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

Substitute server

We run our own substitution server. Add the key to your machine as root with

guix archive --authorize < tux02-guix-substitutions-public-key.txt
guix build -L ~/guix-bioinformatics/ -L ~/guix-past/modules/ genenetwork2 --substitute-urls="https://ci.guix.gnu.org https://bordeaux.guix.gnu.org https://guix.genenetwork.org" --dry-run

LICENSE

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