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Updat Pasteur doc

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Remi Planel 2019-07-30 16:12:30 +02:00
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docs/pasteur.md
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@ -8,14 +8,16 @@ To use, run the pipeline with `-profile pasteur`. This will download and launch
## Running the workflow on the Pasteur cluster ## Running the workflow on the Pasteur cluster
>Nextflow is not installed by default 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 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. 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: The compute nodes don't have access to internet so you need to run it offline.
1. Create a virtualenv to install nf-core in order to get the workflow
To do that:
1. Create a virtualenv to install nf-core
```bash ```bash
module purge module purge
module load Python/3.6.0 module load Python/3.6.0