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56 lines
2 KiB
Markdown
56 lines
2 KiB
Markdown
# nf-core/configs: Institut Pasteur Configuration
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All nf-core pipelines have been successfully configured for use on the tars cluster at the Institut Pasteur.
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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.
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## Running the workflow on the Pasteur cluster
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Nextflow is not installed by default on the Pasteur cluster.
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- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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Nextflow manages each process as a separate job that is submitted to the cluster by using the `sbatch` command.
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Nextflow shouldn't run directly on the submission node but on a compute node.
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The compute nodes don't have access to internet so you need to run it offline.
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To do that:
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1. Create a virtualenv to install nf-core
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```bash
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module purge
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module load Python/3.6.0
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module load java
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module load singularity
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cd /path/to/nf-core/workflows
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virtualenv .venv -p python3
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. .venv/bin/activate
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```
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2. Install nf-core: [here](https://nf-co.re/tools#installation)
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3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use)
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4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base)
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5. Run nextflow on a compute node:
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```bash
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# create a terminal
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tmux
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# Get a compute node
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salloc
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# Load the dependencies if not done before
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module purge
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module load java
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module load singularity
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# Run nextflow workflow
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nextflow run \\
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/path/to/pipeline-dir/from/step/3/workflow \\
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-resume
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-profile pasteur \\
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-with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\
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--email my-email@pasteur.fr \\
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--custom_config_base /path/to/configs/from/step/4/ \\
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-c my-specific.config
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```
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