Merge pull request #58 from rplanel/master

Add Institut Pasteur config

.gitignore

@@ -3,3 +3,4 @@ work/
 data/
 results/
 .DS_Store
+*.code-workspace

README.md

@@ -99,6 +99,7 @@ Currently documentation is available for the following clusters:
 * [UPPMAX-DEVEL](docs/uppmax-devel.md)
 * [UPPMAX](docs/uppmax.md)
 * [UZH](docs/uzh.md)
+* [PASTEUR](docs/pasteur.md)
 
 ### Uploading to `nf-core/configs`
 

conf/pasteur.config

@@ -0,0 +1,23 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'The Institut Pasteur HPC cluster profile'
+  config_profile_contact = 'Remi Planel (@rplanel)'
+  config_profile_url = 'https://research.pasteur.fr/en/service/tars-cluster'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  runOptions = '-B /local/scratch:/tmp'
+}
+
+process {
+  executor = 'slurm'
+}
+
+params {
+  igenomesIgnore = true
+  max_memory = 256.GB
+  max_cpus = 28
+  max_time = 24.h
+}

docs/pasteur.md

@@ -0,0 +1,56 @@
+# 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
+...
+```

nfcore_custom.config

@@ -34,6 +34,7 @@ profiles {
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }
   prince       { includeConfig "${params.custom_config_base}/conf/prince.config" }
   bigpurple    { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
+  pasteur      { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
 }
 
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