Merge pull request #86 from genotoul-bioinfo/master

Add genotoul config

.github/workflows/main.yml

@@ -16,7 +16,8 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-            profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax_devel', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax_devel', 'uppmax', 'uzh']
+
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -97,6 +97,7 @@ Currently documentation is available for the following systems:
 * [CZBIOHUB_AWS](docs/czbiohub.md)
 * [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
 * [DENBI_QBIC](docs/denbi_qbic.md)
+* [GENOTOUL](docs/genotoul.md)
 * [GENOUEST](docs/genouest.md)
 * [GIS](docs/gis.md)
 * [HEBBE](docs/hebbe.md)

conf/genotoul.config

@@ -0,0 +1,26 @@
+//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 {
+  save_reference = true
+  igenomes_ignore = true
+  // Max resources requested by a normal node on genotoul.
+  max_memory = 120.GB
+  max_cpus = 48
+  max_time = 96.h
+}

docs/genotoul.md

@@ -0,0 +1,88 @@
+# 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 :
+
+```bash
+# Login to a compute node
+srun --mem=4G --pty bash
+```
+
+Setup default nextflow and singularity home directory (to be done only one time):
+
+```bash
+sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh
+```
+
+Load environment :
+
+```bash
+module purge
+module load bioinfo/nfcore-Nextflow-v19.04.0
+```
+
+Try a test workflow (for example the methylseq workflow) :
+
+```bash
+nextflow run nf-core/methylseq -profile genotoul,test
+```
+
+Create launch script `nfcore-rnaseq.sh` :
+
+```bash
+#!/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:
+
+```bash
+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 which contain:
+
+```bash
+singularity.runOptions = '-B /directory/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/](http://bioinfo.genotoul.fr/).

nfcore_custom.config

@@ -22,8 +22,10 @@ profiles {
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
-  czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; 
+  czbiohub_aws_highpriority { 
-                              includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
+                 includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; 
+                 includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"}
+  genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
   denbi_qbic   { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
   genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
@@ -48,6 +50,7 @@ params {
   // This is a groovy map, not a nextflow parameter set
   hostnames = [
     crick: ['.thecrick.org'],
+    genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
     genouest: ['.genouest.org'],
     uppmax: ['.uppmax.uu.se']
   ]