1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-10 20:13:09 +00:00

Merge pull request #73 from abretaud/genouest

Add Genouest cluster
This commit is contained in:
Alexander Peltzer 2019-10-17 13:18:04 +02:00 committed by GitHub
commit 2b99228ce8
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
4 changed files with 64 additions and 0 deletions

View file

@ -91,6 +91,7 @@ Currently documentation is available for the following clusters:
* [CRICK](docs/crick.md)
* [CZBIOHUB_AWS](docs/czbiohub.md)
* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
* [GENOUEST](docs/genouest.md)
* [GIS](docs/gis.md)
* [HEBBE](docs/hebbe.md)
* [KRAKEN](docs/kraken.md)

23
conf/genouest.config Normal file
View file

@ -0,0 +1,23 @@
//Profile config names for nf-core/configs
params {
config_profile_description = 'The GenOuest cluster profile'
config_profile_contact = 'Anthony Bretaudeau (@abretaud)'
config_profile_url = 'https://www.genouest.org'
}
singularity {
enabled = true
autoMounts = true
runOptions = '-B /scratch:/scratch -B /local:/local -B /db:/db'
}
process {
executor = 'slurm'
}
params {
igenomesIgnore = true
max_memory = 750.GB
max_cpus = 80
max_time = 336.h
}

38
docs/genouest.md Normal file
View file

@ -0,0 +1,38 @@
# nf-core/configs: GenOuest Configuration
All nf-core pipelines have been successfully configured for use on the GenOuest cluster.
To use, run the pipeline with `-profile genouest`. This will download and launch the [`genouest.config`](../conf/genouest.config) which has been pre-configured with a setup suitable for the GenOuest cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
## Running the workflow on the GenOuest cluster
Nextflow is installed on the GenOuest cluster. Some documentation is available on the [GenOuest website](https://www.genouest.org/howto/#nextflow).
You need to activate it like this:
```bash
source /local/env/envnextflow-19.07.0.sh
```
Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
Nextflow shouldn't run directly on the submission node but on a compute node. Run nextflow from a compute node:
```bash
# Login to a compute node
srun --pty bash
# Load the dependencies if not done before
source /local/env/envnextflow-19.07.0.sh
# Run a downloaded/git-cloned nextflow workflow from
nextflow run \\
/path/to/nf-core/workflow \\
-resume
-profile genouest \\
--email my-email@example.org \\
-c my-specific.config
...
# Or use the nf-core client
nextflow run nf-core/rnaseq ...
```

View file

@ -21,6 +21,7 @@ profiles {
crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" }
gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" }
@ -43,6 +44,7 @@ params {
// This is a groovy map, not a nextflow parameter set
hostnames = [
crick: ['.thecrick.org'],
genouest: ['.genouest.org'],
uppmax: ['.uppmax.uu.se']
]
}