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