From db51c49b2f04e2a39249a7c36aedddfc2f93f913 Mon Sep 17 00:00:00 2001
From: noirot <celine.noirot@inra.fr>
Date: Mon, 25 Nov 2019 14:54:25 +0100
Subject: [PATCH] Add genotoul config

---
 conf/genotoul.config | 27 ++++++++++++++
 docs/genotoul.md     | 85 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 112 insertions(+)
 create mode 100644 conf/genotoul.config
 create mode 100644 docs/genotoul.md

diff --git a/conf/genotoul.config b/conf/genotoul.config
new file mode 100644
index 0000000..588028d
--- /dev/null
+++ b/conf/genotoul.config
@@ -0,0 +1,27 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'The Genotoul cluster profile'
+  config_profile_contact = 'support.bioinfo.genotoul@inra.fr'
+  config_profile_url = 'http://bioinfo.genotoul.fr/'
+}
+
+singularity {
+  // need one image per execution
+  enabled = true
+  runOptions = '-B /bank -B /work2 -B /work -B /save -B /home'
+  
+}
+
+process {
+  executor = 'slurm'
+}
+
+params {
+  saveReference = true
+  igenomesIgnore = true
+  // Max resources requested by a normal node on genotoul.
+  max_memory = 120.GB
+  max_cpus = 48
+  max_time = 96.h
+}
+
diff --git a/docs/genotoul.md b/docs/genotoul.md
new file mode 100644
index 0000000..026a59c
--- /dev/null
+++ b/docs/genotoul.md
@@ -0,0 +1,85 @@
+
+
+
+# nf-core/configs: Bioinfo Genotoul Configuration
+
+All nf-core pipelines have been successfully configured for use on the Bioinfo Genotoul cluster at the INRA toulouse.
+
+To use, run the pipeline with `-profile genotoul`. This will download and
+launch the [`genotoul.config`](../conf/genotoul.config) which has been
+pre-configured with a setup suitable for the Bioinfo Genotoul 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. Images are stored for all users in following directory `/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/`.
+
+## Running the workflow ib the Genologin cluster.
+
+Before running the pipeline you will need to load Nextflow and
+Singularity using the environment module system on Genotoul. You can do
+this by issuing the commands below:
+
+
+Once connected on our frontal node :
+```
+# Login to a compute node
+srun --mem=4G --pty bash
+```
+
+Setup default nextflow and singularity home directory (to be done only one time):
+```
+sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh
+```
+
+Load environment :
+```
+module purge
+module load bioinfo/nfcore-Nextflow-v19.04.0
+```
+
+Try a test workflow (for example the methylseq workflow) :
+```
+nextflow run nf-core/methylseq -profile genotoul,test
+```
+
+Create launch script `nfcore-rnaseq.sh` :
+```
+#!/bin/bash
+#SBATCH -p workq
+#SBATCH -t 1:00:00  #time in hour
+#SBATCH --mem=4G
+#SBATCH --mail-type=BEGIN,END,FAIL
+
+module load bioinfo/nfcore-Nextflow-v19.04.0
+nextflow run nf-core/methylseq -profile genotoul,test
+```
+Launch on the cluster with sbatch:
+```
+sbatch nfcore-rnaseq.sh
+```
+
+## Mounted directory
+
+By default, available mount points are :
+ - /bank
+ - /home
+ - /save
+ - /work  
+ - /work2  
+
+
+To have access to specific other mount point (such as nosave or project)
+you can add a config profile file with option `-profile` and wich contain:
+```
+singularity.runOptions = '-B /diretory/to/mount'
+```
+
+## Databanks
+
+A local copy of several genomes are available in `/bank` directory. See
+our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/)
+to search for your favorite genome.
+
+
+>NB: You will need an account to use the HPC cluster on Genotoul in order
+to run the pipeline. If in doubt see http://bioinfo.genotoul.fr/.