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89 lines
2.4 KiB
Markdown
89 lines
2.4 KiB
Markdown
# nf-core/configs: Bioinfo Genotoul Configuration
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All nf-core pipelines have been successfully configured for use on the Bioinfo Genotoul cluster at the INRA toulouse.
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To use, run the pipeline with `-profile genotoul`. This will download and
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launch the [`genotoul.config`](../conf/genotoul.config) which has been
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pre-configured with a setup suitable for the Bioinfo Genotoul cluster.
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Using this profile, a docker image containing all of the required software
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will be downloaded, and converted to a Singularity image before execution
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of the pipeline. Images are stored for all users in following directory `/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/`.
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## Running the workflow ib the Genologin cluster
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Before running the pipeline you will need to load Nextflow and
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Singularity using the environment module system on Genotoul. You can do
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this by issuing the commands below:
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Once connected on our frontal node :
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```bash
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# Login to a compute node
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srun --mem=4G --pty bash
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```
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Setup default nextflow and singularity home directory (to be done only one time):
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```bash
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sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh
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```
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Load environment :
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```bash
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module purge
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module load bioinfo/nfcore-Nextflow-v19.04.0
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```
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Try a test workflow (for example the methylseq workflow) :
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```bash
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nextflow run nf-core/methylseq -profile genotoul,test
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```
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Create launch script `nfcore-rnaseq.sh` :
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```bash
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#!/bin/bash
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#SBATCH -p workq
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#SBATCH -t 1:00:00 #time in hour
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#SBATCH --mem=4G
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#SBATCH --mail-type=BEGIN,END,FAIL
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module load bioinfo/nfcore-Nextflow-v19.04.0
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nextflow run nf-core/methylseq -profile genotoul,test
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```
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Launch on the cluster with sbatch:
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```bash
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sbatch nfcore-rnaseq.sh
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```
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## Mounted directory
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By default, available mount points are:
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- /bank
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- /home
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- /save
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- /work
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- /work2
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To have access to specific other mount point (such as nosave or project)
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you can add a config profile file with option `-profile` and which contain:
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```bash
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singularity.runOptions = '-B /directory/to/mount'
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```
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## Databanks
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A local copy of several genomes are available in `/bank` directory. See
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our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/)
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to search for your favorite genome.
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> NB: You will need an account to use the HPC cluster on Genotoul in order
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> to run the pipeline. If in doubt see [http://bioinfo.genotoul.fr/](http://bioinfo.genotoul.fr/).
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