From 7e9f83ee8133993c4d14b1c1562644427e51655b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Noirot=20C=C3=A9line?= Date: Tue, 16 Mar 2021 15:54:19 +0100 Subject: [PATCH 1/3] Add IFB config --- .github/workflows/main.yml | 2 +- conf/ifb_core.config | 24 +++++++++++++++++++++++ docs/ifb_core.md | 40 ++++++++++++++++++++++++++++++++++++++ nfcore_custom.config | 1 + 4 files changed, 66 insertions(+), 1 deletion(-) create mode 100644 conf/ifb_core.config create mode 100644 docs/ifb_core.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 3e5c930..cf00bea 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/conf/ifb_core.config b/conf/ifb_core.config new file mode 100644 index 0000000..50a72f4 --- /dev/null +++ b/conf/ifb_core.config @@ -0,0 +1,24 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'The IFB core cluster profile' + config_profile_contact = 'https://community.france-bioinformatique.fr' + config_profile_url = 'https://www.france-bioinformatique.fr/' +} + +singularity { + // need one image per execution + enabled = true + runOptions = '-B /shared' +} + +process { + executor = 'slurm' +} + +params { + igenomes_ignore = true + // Max resources requested by a normal node on genotoul. + max_memory = 240.GB + max_cpus = 28 + max_time = 96.h +} diff --git a/docs/ifb_core.md b/docs/ifb_core.md new file mode 100644 index 0000000..0434a09 --- /dev/null +++ b/docs/ifb_core.md @@ -0,0 +1,40 @@ +# nf-core/configs: IFB core Configuration + +All nf-core pipelines have been successfully configured for use on the IFB core at the insert institution here. + +To use, run the pipeline with `-profile ifb_core`. This will download and launch the [`ifb_core.config`](../conf/ifb_core.config) which has been pre-configured with a setup suitable for the IFB core 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. + +## How to use on IFB core + +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on IFB core. You can do this by issuing the commands below: + +```bash +# Login to a compute node +srun --pty bash + +## Load Nextflow and Singularity environment modules +module purge +module load nextflow/20.04.1 + +# Run a downloaded/git-cloned nextflow workflow from +nextflow run \\ +nf-core/workflow \\ +-resume +-profile ifb_core \\ +--email my-email@example.org \\ +-c my-specific.config +... + + +# Or use the nf-core client +nextflow run nf-core/rnaseq ... + +``` + +## Databanks + +A local copy of several genomes are available in `/shared/bank` directory. See +our [databank page](https://ifb-elixirfr.gitlab.io/cluster/doc/banks/) +to search for your favorite genome. + +>NB: You will need an account to use the HPC cluster on IFB core in order to run the pipeline. If in doubt contact IT or go to [account page](https://my.cluster.france-bioinformatique.fr/manager2/login). diff --git a/nfcore_custom.config b/nfcore_custom.config index 429e3c1..a4c9939 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -24,6 +24,7 @@ profiles { czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" } icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" } + ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" } imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" } imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" } genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" } From cc17045914a56ec05d06da080bc536d20588631a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Noirot=20C=C3=A9line?= Date: Tue, 16 Mar 2021 15:58:29 +0100 Subject: [PATCH 2/3] Add institution --- docs/ifb_core.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ifb_core.md b/docs/ifb_core.md index 0434a09..3c1f546 100644 --- a/docs/ifb_core.md +++ b/docs/ifb_core.md @@ -1,6 +1,6 @@ # nf-core/configs: IFB core Configuration -All nf-core pipelines have been successfully configured for use on the IFB core at the insert institution here. +All nf-core pipelines have been successfully configured for use on the cluster of the IFB (Institut Francais de Bioinformatique). To use, run the pipeline with `-profile ifb_core`. This will download and launch the [`ifb_core.config`](../conf/ifb_core.config) which has been pre-configured with a setup suitable for the IFB core 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. From e3216ccf79aa60edcb8edd30fa8e2618171de90b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Noirot=20C=C3=A9line?= Date: Tue, 16 Mar 2021 16:00:56 +0100 Subject: [PATCH 3/3] typo --- docs/ifb_core.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ifb_core.md b/docs/ifb_core.md index 3c1f546..90c0eb1 100644 --- a/docs/ifb_core.md +++ b/docs/ifb_core.md @@ -6,7 +6,7 @@ To use, run the pipeline with `-profile ifb_core`. This will download and launch ## How to use on IFB core -Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on IFB core. You can do this by issuing the commands below: +Before running the pipeline you will need to load Nextflow using the environment module system on IFB core. You can do this by issuing the commands below: ```bash # Login to a compute node