From db51c49b2f04e2a39249a7c36aedddfc2f93f913 Mon Sep 17 00:00:00 2001 From: noirot Date: Mon, 25 Nov 2019 14:54:25 +0100 Subject: [PATCH 01/13] 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/. From 42d968fd2a9274a457dcbc80dea61a0bc5170228 Mon Sep 17 00:00:00 2001 From: noirot Date: Mon, 25 Nov 2019 16:23:25 +0100 Subject: [PATCH 02/13] add genotoul in nfcore_custom --- nfcore_custom.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index 06182f5..017d326 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -21,6 +21,7 @@ profiles { crick { includeConfig "${params.custom_config_base}/conf/crick.config" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" } + genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" } genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" } gis { includeConfig "${params.custom_config_base}/conf/gis.config" } hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" } @@ -44,6 +45,7 @@ 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'] ] From 9e5b76827fc7e3c6dafc1af8a2b69be068bf0761 Mon Sep 17 00:00:00 2001 From: noirot Date: Mon, 25 Nov 2019 16:37:00 +0100 Subject: [PATCH 03/13] add genotoul in README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index b9812b6..cb7e3d4 100644 --- a/README.md +++ b/README.md @@ -93,6 +93,7 @@ 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) From 42d99e700666972ad03dc8fda0b81784cc9d8eeb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Noirot=20C=C3=A9line?= Date: Tue, 26 Nov 2019 13:18:34 +0100 Subject: [PATCH 04/13] Update genotoul.md --- docs/genotoul.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/docs/genotoul.md b/docs/genotoul.md index 026a59c..47e1916 100644 --- a/docs/genotoul.md +++ b/docs/genotoul.md @@ -1,6 +1,3 @@ - - - # 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. From 42c949db95947490733d5aec4c150760102006ef Mon Sep 17 00:00:00 2001 From: noirot Date: Tue, 26 Nov 2019 14:43:42 +0100 Subject: [PATCH 05/13] correct md to pass linter --- docs/genotoul.md | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/docs/genotoul.md b/docs/genotoul.md index 47e1916..831e90e 100644 --- a/docs/genotoul.md +++ b/docs/genotoul.md @@ -10,37 +10,41 @@ 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. +## 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 @@ -51,7 +55,8 @@ 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 ``` @@ -64,10 +69,9 @@ By default, available mount points are : - /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: -``` +```bash singularity.runOptions = '-B /diretory/to/mount' ``` @@ -77,6 +81,5 @@ 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/. +to run the pipeline. If in doubt see [http://bioinfo.genotoul.fr/](http://bioinfo.genotoul.fr/). From e95196451fe850201e0b471e2b3cc81d78e210b3 Mon Sep 17 00:00:00 2001 From: noirot Date: Tue, 26 Nov 2019 14:47:23 +0100 Subject: [PATCH 06/13] correct md to pass linter --- docs/genotoul.md | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/docs/genotoul.md b/docs/genotoul.md index 831e90e..5f46f21 100644 --- a/docs/genotoul.md +++ b/docs/genotoul.md @@ -54,6 +54,7 @@ Create launch script `nfcore-rnaseq.sh` : module load bioinfo/nfcore-Nextflow-v19.04.0 nextflow run nf-core/methylseq -profile genotoul,test ``` + Launch on the cluster with sbatch: ```bash @@ -63,14 +64,15 @@ sbatch nfcore-rnaseq.sh ## Mounted directory By default, available mount points are : - - /bank - - /home - - /save - - /work - - /work2 +- /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: + ```bash singularity.runOptions = '-B /diretory/to/mount' ``` From dd4ff452dac7efc00fd04501a460656b1595272f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Noirot=20C=C3=A9line?= Date: Tue, 26 Nov 2019 14:49:47 +0100 Subject: [PATCH 07/13] Update conf/genotoul.config Co-Authored-By: Maxime Garcia --- conf/genotoul.config | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/conf/genotoul.config b/conf/genotoul.config index 588028d..e5a1242 100644 --- a/conf/genotoul.config +++ b/conf/genotoul.config @@ -18,10 +18,9 @@ process { params { saveReference = true - igenomesIgnore = true + igenomes_ignore = true // Max resources requested by a normal node on genotoul. max_memory = 120.GB max_cpus = 48 max_time = 96.h } - From 611c318569c4d9d4683052ec1d8009c41d05f981 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Noirot=20C=C3=A9line?= Date: Tue, 26 Nov 2019 14:50:05 +0100 Subject: [PATCH 08/13] Update conf/genotoul.config Co-Authored-By: Maxime Garcia --- conf/genotoul.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/genotoul.config b/conf/genotoul.config index e5a1242..75ad2c4 100644 --- a/conf/genotoul.config +++ b/conf/genotoul.config @@ -17,7 +17,7 @@ process { } params { - saveReference = true + save_reference = true igenomes_ignore = true // Max resources requested by a normal node on genotoul. max_memory = 120.GB From 288294994e0c9df795cc34c71464ae8a40663e9b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Noirot=20C=C3=A9line?= Date: Tue, 26 Nov 2019 14:52:32 +0100 Subject: [PATCH 09/13] Update docs/genotoul.md ok Co-Authored-By: Maxime Garcia --- docs/genotoul.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/genotoul.md b/docs/genotoul.md index 5f46f21..e6b2f13 100644 --- a/docs/genotoul.md +++ b/docs/genotoul.md @@ -71,7 +71,7 @@ By default, available mount points are : - /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: +you can add a config profile file with option `-profile` and which contain: ```bash singularity.runOptions = '-B /diretory/to/mount' From 3ed206b7a773efdde19e6291e41cd7ecb6e40f5a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Noirot=20C=C3=A9line?= Date: Tue, 26 Nov 2019 14:52:45 +0100 Subject: [PATCH 10/13] Update docs/genotoul.md ok Co-Authored-By: Maxime Garcia --- docs/genotoul.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/genotoul.md b/docs/genotoul.md index e6b2f13..5fe02b7 100644 --- a/docs/genotoul.md +++ b/docs/genotoul.md @@ -74,7 +74,7 @@ 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 /diretory/to/mount' +singularity.runOptions = '-B /directory/to/mount' ``` ## Databanks From 3d8da62db3c29d0c631f6167112208e3fdd0972a Mon Sep 17 00:00:00 2001 From: noirot Date: Tue, 26 Nov 2019 14:57:17 +0100 Subject: [PATCH 11/13] add genotoul profile name to the build matrix --- .github/workflows/main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d9c2f12..6d3f127 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -6,7 +6,7 @@ jobs: name: Run individual profiles strategy: matrix: - profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'czbiohub_aws_highpriority', 'czbiohub_aws', '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', 'czbiohub_aws_highpriority', 'czbiohub_aws', '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 @@ -17,4 +17,4 @@ jobs: run: | python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml - name: "Check profile" - run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} \ No newline at end of file + run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} From 07b1f17d6a81a145d3c1afde1cf8ebd53b746a4a Mon Sep 17 00:00:00 2001 From: noirot Date: Tue, 26 Nov 2019 15:02:06 +0100 Subject: [PATCH 12/13] correct md to pass linter --- docs/genotoul.md | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/docs/genotoul.md b/docs/genotoul.md index 5fe02b7..b86cf66 100644 --- a/docs/genotoul.md +++ b/docs/genotoul.md @@ -63,12 +63,13 @@ sbatch nfcore-rnaseq.sh ## Mounted directory -By default, available mount points are : -- /bank -- /home -- /save -- /work -- /work2 +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: From 0fdcf8c70c86b18c648cbf303b02514a6fa0cda4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Noirot=20C=C3=A9line?= Date: Tue, 26 Nov 2019 15:10:13 +0100 Subject: [PATCH 13/13] Update .github/workflows/main.yml Co-Authored-By: Alexander Peltzer --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e36b79a..a9d41b5 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'czbiohub_aws_highpriority', 'czbiohub_aws', 'denbi_qbic', 'genotoul', '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