Using Snakemake on the HPC Cluster: Difference between revisions
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Davebridges (talk | contribs) Created initial coding example for snakemake |
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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 <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: | ||
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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> | ||
Latest revision as of 20:00, 16 May 2024
Setup
- 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
mamba activate snakemake
- Install the cluster-generic tool to submit snakemake files to a cluster from pip with
pip install snakemake-executor-plugin-cluster-generic
- Create a generic profile in ~/.config/snakemake/testprofile/config.yaml such as:
executor: slurm
jobs: 100
default-resources:
mem_mb: max(1.5 * input.size_mb, 100)
account: <ACCOUNT_NAME>
partition: <PARTITION NAME>
set-threads:
myrule: max(input.size_mb / 5, 2)
set-resources:
myrule:
mem_mb: attempt * 200
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
snakemake --profile testprofile -j 1 --executor cluster-generic --cluster-generic-submit-cmd "batch" ...