Commit 7ac07858 authored by van den Berg's avatar van den Berg
Browse files

Inject slurm submission into integration test

parent d6880eee
Pipeline #3620 passed with stages
in 31 minutes and 46 seconds
......@@ -14,6 +14,12 @@ variables:
- conda activate hutspot-pipeline
- export PATH=${PATH}:${SINGULARITY_PATH}
- echo $BASETEMP
- echo $PATH
- which snakemake
- echo "$(which snakemake) --profile slurm-test \"\$@\"" > snakemake
- chmod +x snakemake
- export PATH=.:${PATH}
stages:
- sanity
......
__default__:
job_name: hutspot
queue: short
vmem: 4G
threads: 1
time: 00:10:00
tmp: 1G
cluster: ' sbatch --parsable --job-name {jobid} --time={cluster.time} -p {cluster.queue} -c {cluster.threads} --mem-per-cpu={cluster.vmem} --tmp={cluster.tmp}'
cluster-config: 'slurm-test/cluster.yaml'
cluster-status: 'cluster/slurm-cluster-status/slurm-cluster-status.py'
jobs: 70
latency-wait: 120
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