mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-12-23 10:58:16 +00:00
56 lines
2 KiB
Markdown
56 lines
2 KiB
Markdown
# nf-core/configs: Institut Pasteur Configuration
|
|
|
|
All nf-core pipelines have been successfully configured for use on the tars cluster at the Institut Pasteur.
|
|
|
|
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.
|
|
|
|
## Running the workflow 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#)
|
|
|
|
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.
|
|
The compute nodes don't have access to internet so you need to run it offline.
|
|
|
|
To do that:
|
|
|
|
1. Create a virtualenv to install nf-core
|
|
|
|
```bash
|
|
module purge
|
|
module load Python/3.6.0
|
|
module load java
|
|
module load singularity
|
|
cd /path/to/nf-core/workflows
|
|
virtualenv .venv -p python3
|
|
. .venv/bin/activate
|
|
```
|
|
|
|
2. Install nf-core: [here](https://nf-co.re/tools#installation)
|
|
3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use)
|
|
4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base)
|
|
5. Run nextflow on a compute node:
|
|
|
|
```bash
|
|
# create a terminal
|
|
tmux
|
|
# Get a compute node
|
|
salloc
|
|
# Load the dependencies if not done before
|
|
module purge
|
|
module load java
|
|
module load singularity
|
|
|
|
# Run nextflow workflow
|
|
nextflow run \\
|
|
/path/to/pipeline-dir/from/step/3/workflow \\
|
|
-resume
|
|
-profile pasteur \\
|
|
-with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\
|
|
--email my-email@pasteur.fr \\
|
|
--custom_config_base /path/to/configs/from/step/4/ \\
|
|
-c my-specific.config
|
|
|
|
```
|