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@@ -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