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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 28 |
1 files changed, 19 insertions, 9 deletions
@@ -5,7 +5,21 @@ http://genenetwork.org/. See [Guix Notes](https://github.com/pjotrp/guix-notes/blob/master/HACKING.org) for installing and hacking GNU Guix. -Simply set the GUIX_PACKAGE_PATH to point to the root of this directory +To easily use the packages from this repo, simply add it to your `channels` list: + + (cons* + (channel + (name 'gn-bioinformatics) + (url "https://gitlab.com/genenetwork/guix-bioinformatics") + (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://github.com/genenetwork/guix-bioinformatics.git @@ -23,8 +37,7 @@ into the GNU Guix repository when tested and stable. Install slurm with - git clone https://github.com/genenetwork/guix-bioinformatics.git - export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/ + guix pull guix package -i slurm-llnl ~/.guix-profile/sbin/slurmd -C -D @@ -34,8 +47,7 @@ Install slurm with Install the module environment with - git clone https://github.com/genenetwork/guix-bioinformatics.git - export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/ + guix pull guix package -i environment-modules modulecmd --version @@ -46,16 +58,14 @@ Install the module environment with Install python2-numarray package with - git clone https://github.com/genenetwork/guix-bioinformatics.git - export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/ + guix pull guix package -i python2-numarray ## Common Workflow Language (CWL) Install the common workflow language tool cwltool with - git clone https://github.com/genenetwork/guix-bioinformatics.git - export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/ + guix pull guix package -i python2-cwltool cwtool --version |