diff --git a/docs/genotoul.md b/docs/genotoul.md index 47e1916..831e90e 100644 --- a/docs/genotoul.md +++ b/docs/genotoul.md @@ -10,37 +10,41 @@ 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. Images are stored for all users in following directory `/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/`. -## Running the workflow ib the Genologin cluster. +## Running the workflow ib the Genologin cluster Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on Genotoul. You can do this by issuing the commands below: - Once connected on our frontal node : -``` + +```bash # Login to a compute node srun --mem=4G --pty bash ``` Setup default nextflow and singularity home directory (to be done only one time): -``` + +```bash sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh ``` Load environment : -``` + +```bash module purge module load bioinfo/nfcore-Nextflow-v19.04.0 ``` Try a test workflow (for example the methylseq workflow) : -``` + +```bash nextflow run nf-core/methylseq -profile genotoul,test ``` Create launch script `nfcore-rnaseq.sh` : -``` + +```bash #!/bin/bash #SBATCH -p workq #SBATCH -t 1:00:00 #time in hour @@ -51,7 +55,8 @@ module load bioinfo/nfcore-Nextflow-v19.04.0 nextflow run nf-core/methylseq -profile genotoul,test ``` Launch on the cluster with sbatch: -``` + +```bash sbatch nfcore-rnaseq.sh ``` @@ -64,10 +69,9 @@ By default, available mount points are : - /work - /work2 - To have access to specific other mount point (such as nosave or project) you can add a config profile file with option `-profile` and wich contain: -``` +```bash singularity.runOptions = '-B /diretory/to/mount' ``` @@ -77,6 +81,5 @@ A local copy of several genomes are available in `/bank` directory. See our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/) to search for your favorite genome. - >NB: You will need an account to use the HPC cluster on Genotoul in order -to run the pipeline. If in doubt see http://bioinfo.genotoul.fr/. +to run the pipeline. If in doubt see [http://bioinfo.genotoul.fr/](http://bioinfo.genotoul.fr/).