diff --git a/conf/binac.config b/conf/binac.config index 9447ca4..e2bce86 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -13,13 +13,14 @@ process { beforeScript = 'module load devel/singularity/3.0.3' executor = 'pbs' queue = 'short' + process.queue = { task.memory > 128.GB ? 'smp': task.time <= 20m ? 'tiny' : task.time <= 48.h ? 'short' : task.time <= 168.h ? 'long'} } params { igenomes_base = '/nfsmounts/igenomes' - max_memory = 128.GB + max_memory = 1024.GB max_cpus = 28 - max_time = 48.h + max_time = 168.h } weblog{ diff --git a/docs/pasteur.md b/docs/pasteur.md index 554761b..6e2d825 100644 --- a/docs/pasteur.md +++ b/docs/pasteur.md @@ -4,36 +4,38 @@ All nf-core pipelines have been successfully configured for use on the tars clus To use, run the pipeline with `-profile pasteur`. This will download and launch the [`pasteur.config`](../conf/pasteur.config) which has been pre-configured with a setup suitable for the Pasteur 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 Pasteur cluster Nextflow is not installed by default on the Pasteur cluster. -- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) +- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) 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. The compute nodes don't have access to internet so you need to run it offline. To do that: + 1. Create a virtualenv to install nf-core -```bash -module purge -module load Python/3.6.0 -module load java -module load singularity -cd /path/to/nf-core/workflows -virtualenv .venv -p python3 -. .venv/bin/activate -``` + + ```bash + module purge + module load Python/3.6.0 + module load java + module load singularity + cd /path/to/nf-core/workflows + virtualenv .venv -p python3 + . .venv/bin/activate + ``` + 2. Install nf-core: [here](https://nf-co.re/tools#installation) 3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use) -4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base) -5. Run nextflow on a compute node: +4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/configs#offline-usage) +5. Run nextflow on a compute node: + ```bash # create a terminal -tmux +tmux # Get a compute node salloc @@ -46,7 +48,7 @@ module load singularity # Run nextflow workflow nextflow run \\ /path/to/pipeline-dir/from/step/3/workflow \\ --resume +-resume -profile pasteur \\ -with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\ --email my-email@pasteur.fr \\