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Add ABiMS - NXF_SINGULARITY_CACHEDIR

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lecorguille 2020-10-22 23:17:55 +02:00
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docs/abims.md
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@ -16,7 +16,7 @@ Nextflow is installed on the ABiMS cluster. Some documentation is available on t
You need to activate it like this: You need to activate it like this:
```bash ```bash
module load nextflow/20.04.1 slurm-drmaa/1.0.8 module load nextflow slurm-drmaa graphviz
``` ```
Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command. Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
@ -27,7 +27,7 @@ Nextflow shouldn't run directly on the submission node but on a compute node. Ru
srun --pty bash srun --pty bash
# Load the dependencies if not done before # Load the dependencies if not done before
module load nextflow/20.04.1 slurm-drmaa/1.0.8 module load nextflow slurm-drmaa graphviz
# Run a downloaded/git-cloned nextflow workflow from # Run a downloaded/git-cloned nextflow workflow from
nextflow run \\ nextflow run \\
@ -42,6 +42,12 @@ nextflow run \\
nextflow run nf-core/rnaseq ... nextflow run nf-core/rnaseq ...
``` ```
## Singularity images mutualized directory
To reduce the disk usage, nf-core images can be stored in a mutualized directory: `/shared/software/singularity/images/nf-core/`
The environment variable `NXF_SINGULARITY_CACHEDIR: /shared/data/cache/nextflow` will indicate this directory to nextflow.
## Databanks ## Databanks
A local copy of several genomes are available in `/shared/bank` directory. A local copy of several genomes are available in `/shared/bank/` directory.