Using Snakemake on the HPC Cluster: Difference between revisions
Created initial coding example for snakemake |
Switched back |
||
| (One intermediate revision by the same user not shown) | |||
| Line 3: | Line 3: | ||
* 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 <pre>mamba activate snakemake</pre> | * 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 <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: | ||
| Line 19: | Line 20: | ||
mem_mb: attempt * 200 | mem_mb: attempt * 200 | ||
</pre> | </pre> | ||
== 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 <pre>snakemake --profile testprofile -j 1 --executor cluster-generic --cluster-generic-submit-cmd "batch" ... </pre> | * Run the Snakefile with this command <pre>snakemake --profile testprofile -j 1 --executor cluster-generic --cluster-generic-submit-cmd "batch" ... </pre> | ||