Use Snakemake's `--cluster` flag instead of `--drmaa`
Since the last local cluster upgrade, we no longer have support for DRMAA. Even
though this interface is _much_ faster than the file-based `--cluster`
interface, it's easier at this point to stop bothering SciComp and get on with
our lives however slightly slowly.
@@ -28,12 +28,12 @@ cluster-config: nextstrain_profiles/nextstrain-rhino/cluster.json
# with this key tells SLURM how to map cluster resources with those defined in
# the cluster config above.
default-resources: mem_mb=256
-drmaa: " {cluster.partition} --nodes=1 --ntasks=1 --mem={resources.mem_mb} --cpus-per-task={threads} --time={cluster.time}"
+#drmaa: " {cluster.partition} --nodes=1 --ntasks=1 --mem={resources.mem_mb} --cpus-per-task={threads} --time={cluster.time}"
# NOTE: Use the settings from the next block if DRMAA is not an option.
# Use a custom script to evaluate the status of jobs on the cluster. This
# prevents jobs from dying silently and not being caught by Snakemake.
-#cluster: "sbatch {cluster.partition} --nodes=1 --ntasks=1 --mem={cluster.memory} --cpus-per-task={cluster.cores} --tmp={cluster.disk} --time={cluster.time}"
+cluster: "sbatch {cluster.partition} --nodes=1 --ntasks=1 --mem={resources.mem_mb} --cpus-per-task={threads} --time={cluster.time}"
#cluster-status: "slurm-status.py"
# Wait a fixed number of seconds for missing files since the cluster file system
