Commit 5399fc25 authored by Sander Bollen's avatar Sander Bollen
Browse files

move sge cluster to cluster subdirectory

parent a7ee85d4
......@@ -135,20 +135,20 @@ The following configuration options are **optional**:
To run on a cluster, snakemake needs to be called with some extra arguments.
Additionally, it needs a cluster yaml file describing resources per job.
In all cases, an environment variable named `DRMAA_LIBRARY_PATH` must be
in the executing shell environment. This variable points to the `.so` file
of the DRMAA library.
A cluster.yml is bundled with this pipeline. It is optimized for SGE clusters,
where the default vmem limit is 4G. If you run SLURM, or any other cluster
system, you will have to write your own cluster yaml file. Please see the
[snakemake documentation](http://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html#cluster-configuration)
for details on how to do so. Given the provided cluster.yml, activating the
If you run on a cluster with drmaa support,an environment variable named
`DRMAA_LIBRARY_PATH` must be in the executing shell environment. This variable
points to the `.so` file of the DRMAA library.
An sge-cluster.yml is bundled with this pipeline in the cluster directory.
It is optimized for SGE clusters, where the default vmem limit is 4G.
If you run SLURM, or any other cluster system, you will have to write your own
cluster yaml file. Please see the [snakemake documentation](http://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html#cluster-configuration)
for details on how to do so. Given the provided sge-cluster.yml, activating the
cluster mode can be done as follows:
```bash
snakemake -s Snakefile \
--cluster-config cluster.yml
--cluster-config cluster/sge-cluster.yml
--drmaa ' -pe <PE_NAME> {cluster.threads} -q all.q -l h_vmem={cluster.vmem} -cwd -V -N hutspot' \
```
......@@ -159,7 +159,7 @@ To sum up, a full pipeline run under a cluster would be called as:
```bash
snakemake -s Snakefile \
--use-conda \
--cluster-config cluster.yml \
--cluster-config cluster/sge-cluster.yml \
--drmaa ' -pe <PE_NAME> {cluster.threads} -q all.q -l h_vmem={cluster.vmem} -cwd -V -N hutspot' \
--rerun-incomplete \
--jobs 200 \
......
__default__:
job_name: hutspot
threads: 1
vmem: 4G
queue: all.q
align:
threads: 8
vmem: 4G
markdup:
vmem: 10G
baserecal:
threads: 8
vmem: 6G
printreads:
vmem: 10G
gvcf_scatter:
vmem: 20G
gvcf_gather:
vmem: 10G
genotype_scatter:
vmem: 20G
genotype_gather:
vmem: 10G
covstats:
vmem: 6G
multiqc:
vmem: 20G
split_vcf:
vmem: 20G
- name: test-integration-run
- name: test-functional-run
command: >-
bash -c '
snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
......
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