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Diffstat (limited to 'README.org')
| -rw-r--r-- | README.org | 60 |
1 files changed, 49 insertions, 11 deletions
@@ -58,31 +58,69 @@ Install slurm with ClusterName=(null) NodeName=selinunte CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=2 ThreadsPerCore=2 RealMemory=7890 TmpDisk=29909 #+END_SRC -* Module system -Install the module environment with +* Common Workflow Language (CWL) + +Install the common workflow language tool cwltool from this repo with #+BEGIN_SRC bash + guix pull - guix package -i environment-modules + 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 - modulecmd --version - VERSION=3.2.10 - DATE=2012-12-21 +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 #+END_SRC -* Common Workflow Language (CWL) +To run CWL definitions you can install tools in a Guix environment (avoiding +Docker). Say you need mafft in a workflow + +#+begin_src sh + ~/guix-bioinformatics$ env GUIX_PACKAGE_PATH=.:../guix-past/modules/ ~/.config/guix/current/bin/guix environment \ + guix --ad-hoc cwl-runner mafft +#+end_src -Install the common workflow language tool cwltool with +in the new shell you should be able to find both CWL and MAFFT: + +#+begin_src sh +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 +#+end_src + +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 #+BEGIN_SRC bash guix pull - guix package -i python2-cwltool + guix package -i environment-modules - cwtool --version - 1.0.20150916041152 + modulecmd --version + VERSION=3.2.10 + DATE=2012-12-21 #+END_SRC +Note that GNU Guix supercedes module functionality! + * Development tips ** Override individual packages |