915
edits
Changes
Switched back
* Install snakemake via mamba/conda (see https://snakemake.readthedocs.io/en/stable/getting_started/installation.html)
* In the working folder create a snakemake environment with <codepre>mamba activate snakemake</cpdepre>* Install the cluster-generic tool to submit snakemake files to a cluster from pip with <codepre>pip install snakemake-executor-plugin-cluster-generic</codepre>
* Create a generic profile in ~/.config/snakemake/testprofile/config.yaml such as:
<codepre>
executor: slurm
jobs: 100
myrule:
mem_mb: attempt * 200
</codepre>
== Executing a Snakefile Workflow ==
* Create a Snakefile (see
** You can over-ride resources with that flag otherwise it will use the values in testprofile
* Run the Snakefile with this command <codepre>snakemake --profile testprofile -j 1 --executor cluster-generic --cluster-generic-submit-cmd "batch" ... </codepre>