diff --git a/README.md b/README.md index af4aad1..5323165 100644 --- a/README.md +++ b/README.md @@ -83,8 +83,8 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs Currently documentation is available for the following clusters: * [AQUILA](docs/aquila.md) -* [BINAC](docs/binac.md) * [BIGPURPLE](docs/bigpurple.md) +* [BINAC](docs/binac.md) * [CCGA](docs/ccga.md) * [CCGA_DX](/docs/ccga_dx.md) * [CFC](docs/binac.md) @@ -98,8 +98,8 @@ Currently documentation is available for the following clusters: * [PRINCE](docs/prince.md) * [SHH](docs/shh.md) * [UCT_HEX](docs/uct_hex.md) -* [UPPMAX-DEVEL](docs/uppmax-devel.md) * [UPPMAX](docs/uppmax.md) +* [UPPMAX-DEVEL](docs/uppmax-devel.md) * [UZH](docs/uzh.md) ### Uploading to `nf-core/configs` diff --git a/docs/pasteur.md b/docs/pasteur.md index 554761b..6e2d825 100644 --- a/docs/pasteur.md +++ b/docs/pasteur.md @@ -4,36 +4,38 @@ All nf-core pipelines have been successfully configured for use on the tars clus 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#) +- 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 -``` + + ```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: +4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/configs#offline-usage) +5. Run nextflow on a compute node: + ```bash # create a terminal -tmux +tmux # Get a compute node salloc @@ -46,7 +48,7 @@ module load singularity # Run nextflow workflow nextflow run \\ /path/to/pipeline-dir/from/step/3/workflow \\ --resume +-resume -profile pasteur \\ -with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\ --email my-email@pasteur.fr \\ diff --git a/nfcore_custom.config b/nfcore_custom.config index 469d6af..69bb8f3 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -33,8 +33,8 @@ profiles { prince { includeConfig "${params.custom_config_base}/conf/prince.config" } shh { includeConfig "${params.custom_config_base}/conf/shh.config" } uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" } - uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } + uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } }