diff --git a/conf/genotoul.config b/conf/genotoul.config new file mode 100644 index 0000000..588028d --- /dev/null +++ b/conf/genotoul.config @@ -0,0 +1,27 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'The Genotoul cluster profile' + config_profile_contact = 'support.bioinfo.genotoul@inra.fr' + config_profile_url = 'http://bioinfo.genotoul.fr/' +} + +singularity { + // need one image per execution + enabled = true + runOptions = '-B /bank -B /work2 -B /work -B /save -B /home' + +} + +process { + executor = 'slurm' +} + +params { + saveReference = true + igenomesIgnore = true + // Max resources requested by a normal node on genotoul. + max_memory = 120.GB + max_cpus = 48 + max_time = 96.h +} + diff --git a/docs/genotoul.md b/docs/genotoul.md new file mode 100644 index 0000000..026a59c --- /dev/null +++ b/docs/genotoul.md @@ -0,0 +1,85 @@ + + + +# nf-core/configs: Bioinfo Genotoul Configuration + +All nf-core pipelines have been successfully configured for use on the Bioinfo Genotoul cluster at the INRA toulouse. + +To use, run the pipeline with `-profile genotoul`. This will download and +launch the [`genotoul.config`](../conf/genotoul.config) which has been +pre-configured with a setup suitable for the Bioinfo Genotoul 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. Images are stored for all users in following directory `/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/`. + +## 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 : +``` +# Login to a compute node +srun --mem=4G --pty bash +``` + +Setup default nextflow and singularity home directory (to be done only one time): +``` +sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh +``` + +Load environment : +``` +module purge +module load bioinfo/nfcore-Nextflow-v19.04.0 +``` + +Try a test workflow (for example the methylseq workflow) : +``` +nextflow run nf-core/methylseq -profile genotoul,test +``` + +Create launch script `nfcore-rnaseq.sh` : +``` +#!/bin/bash +#SBATCH -p workq +#SBATCH -t 1:00:00 #time in hour +#SBATCH --mem=4G +#SBATCH --mail-type=BEGIN,END,FAIL + +module load bioinfo/nfcore-Nextflow-v19.04.0 +nextflow run nf-core/methylseq -profile genotoul,test +``` +Launch on the cluster with sbatch: +``` +sbatch nfcore-rnaseq.sh +``` + +## Mounted directory + +By default, available mount points are : + - /bank + - /home + - /save + - /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: +``` +singularity.runOptions = '-B /diretory/to/mount' +``` + +## Databanks + +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/.