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Revert "BINAC SMP / Short / Long Updates"

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Alexander Peltzer 2019-10-28 13:12:31 +01:00 committed by GitHub
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5
conf/binac.config
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@ -13,14 +13,13 @@ process {
beforeScript = 'module load devel/singularity/3.0.3' beforeScript = 'module load devel/singularity/3.0.3'
executor = 'pbs' executor = 'pbs'
queue = 'short' queue = 'short'
process.queue = { task.memory > 128.GB ? 'smp': task.time <= 20m ? 'tiny' : task.time <= 48.h ? 'short' : task.time <= 168.h ? 'long'}
} }
params { params {
igenomes_base = '/nfsmounts/igenomes' igenomes_base = '/nfsmounts/igenomes'
max_memory = 1024.GB max_memory = 128.GB
max_cpus = 28 max_cpus = 28
max_time = 168.h max_time = 48.h
} }
weblog{ weblog{

34
docs/pasteur.md
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@ -4,38 +4,36 @@ 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. 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 ## 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. The compute nodes don't have access to internet so you need to run it offline.
To do that: To do that:
1. Create a virtualenv to install nf-core 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 module load java
module load java module load singularity
module load singularity cd /path/to/nf-core/workflows
cd /path/to/nf-core/workflows virtualenv .venv -p python3
virtualenv .venv -p python3 . .venv/bin/activate
. .venv/bin/activate ```
```
2. Install nf-core: [here](https://nf-co.re/tools#installation) 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) 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/configs#offline-usage) 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: 5. Run nextflow on a compute node:
```bash ```bash
# create a terminal # create a terminal
tmux tmux
# Get a compute node # Get a compute node
salloc salloc
@ -48,7 +46,7 @@ module load singularity
# Run nextflow workflow # Run nextflow workflow
nextflow run \\ nextflow run \\
/path/to/pipeline-dir/from/step/3/workflow \\ /path/to/pipeline-dir/from/step/3/workflow \\
-resume -resume
-profile pasteur \\ -profile pasteur \\
-with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\ -with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\
--email my-email@pasteur.fr \\ --email my-email@pasteur.fr \\