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Merge pull request #86 from genotoul-bioinfo/master
Add genotoul config
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commit
caa979f102
5 changed files with 122 additions and 3 deletions
3
.github/workflows/main.yml
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3
.github/workflows/main.yml
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@ -16,7 +16,8 @@ jobs:
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needs: test_all_profiles
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needs: test_all_profiles
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strategy:
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strategy:
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matrix:
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matrix:
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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']
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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']
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steps:
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steps:
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- uses: actions/checkout@v1
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- uses: actions/checkout@v1
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- name: Install Nextflow
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- name: Install Nextflow
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@ -97,6 +97,7 @@ Currently documentation is available for the following systems:
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* [CZBIOHUB_AWS](docs/czbiohub.md)
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* [CZBIOHUB_AWS](docs/czbiohub.md)
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* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
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* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
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* [DENBI_QBIC](docs/denbi_qbic.md)
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* [DENBI_QBIC](docs/denbi_qbic.md)
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* [GENOTOUL](docs/genotoul.md)
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* [GENOUEST](docs/genouest.md)
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* [GENOUEST](docs/genouest.md)
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* [GIS](docs/gis.md)
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* [GIS](docs/gis.md)
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* [HEBBE](docs/hebbe.md)
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* [HEBBE](docs/hebbe.md)
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26
conf/genotoul.config
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26
conf/genotoul.config
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@ -0,0 +1,26 @@
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//Profile config names for nf-core/configs
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params {
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config_profile_description = 'The Genotoul cluster profile'
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config_profile_contact = 'support.bioinfo.genotoul@inra.fr'
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config_profile_url = 'http://bioinfo.genotoul.fr/'
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}
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singularity {
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// need one image per execution
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enabled = true
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runOptions = '-B /bank -B /work2 -B /work -B /save -B /home'
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}
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process {
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executor = 'slurm'
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}
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params {
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save_reference = true
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igenomes_ignore = true
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// Max resources requested by a normal node on genotoul.
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max_memory = 120.GB
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max_cpus = 48
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max_time = 96.h
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}
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88
docs/genotoul.md
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docs/genotoul.md
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@ -0,0 +1,88 @@
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# nf-core/configs: Bioinfo Genotoul Configuration
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All nf-core pipelines have been successfully configured for use on the Bioinfo Genotoul cluster at the INRA toulouse.
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To use, run the pipeline with `-profile genotoul`. This will download and
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launch the [`genotoul.config`](../conf/genotoul.config) which has been
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pre-configured with a setup suitable for the Bioinfo Genotoul cluster.
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Using this profile, a docker image containing all of the required software
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will be downloaded, and converted to a Singularity image before execution
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of the pipeline. Images are stored for all users in following directory `/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/`.
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## Running the workflow ib the Genologin cluster
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Before running the pipeline you will need to load Nextflow and
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Singularity using the environment module system on Genotoul. You can do
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this by issuing the commands below:
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Once connected on our frontal node :
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```bash
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# Login to a compute node
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srun --mem=4G --pty bash
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```
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Setup default nextflow and singularity home directory (to be done only one time):
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```bash
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sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh
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```
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Load environment :
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```bash
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module purge
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module load bioinfo/nfcore-Nextflow-v19.04.0
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```
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Try a test workflow (for example the methylseq workflow) :
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```bash
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nextflow run nf-core/methylseq -profile genotoul,test
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```
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Create launch script `nfcore-rnaseq.sh` :
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```bash
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#!/bin/bash
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#SBATCH -p workq
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#SBATCH -t 1:00:00 #time in hour
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#SBATCH --mem=4G
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#SBATCH --mail-type=BEGIN,END,FAIL
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module load bioinfo/nfcore-Nextflow-v19.04.0
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nextflow run nf-core/methylseq -profile genotoul,test
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```
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Launch on the cluster with sbatch:
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```bash
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sbatch nfcore-rnaseq.sh
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```
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## Mounted directory
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By default, available mount points are:
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* /bank
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* /home
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* /save
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* /work
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* /work2
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To have access to specific other mount point (such as nosave or project)
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you can add a config profile file with option `-profile` and which contain:
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```bash
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singularity.runOptions = '-B /directory/to/mount'
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```
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## Databanks
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A local copy of several genomes are available in `/bank` directory. See
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our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/)
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to search for your favorite genome.
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>NB: You will need an account to use the HPC cluster on Genotoul in order
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to run the pipeline. If in doubt see [http://bioinfo.genotoul.fr/](http://bioinfo.genotoul.fr/).
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@ -22,8 +22,10 @@ profiles {
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cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
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cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
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crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
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crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
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czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
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czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
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czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
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czbiohub_aws_highpriority {
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includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
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includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
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includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"}
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genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
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denbi_qbic { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
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denbi_qbic { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
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genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" }
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genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" }
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gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
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gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
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@ -48,6 +50,7 @@ params {
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// This is a groovy map, not a nextflow parameter set
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// This is a groovy map, not a nextflow parameter set
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hostnames = [
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hostnames = [
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crick: ['.thecrick.org'],
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crick: ['.thecrick.org'],
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genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
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genouest: ['.genouest.org'],
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genouest: ['.genouest.org'],
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uppmax: ['.uppmax.uu.se']
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uppmax: ['.uppmax.uu.se']
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]
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]
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