From 1608b36dcf0624302b065f60bb75b9b2f23ce487 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Tue, 2 Feb 2021 17:40:10 +0900 Subject: [PATCH] Institutional profile for Okinawa Institute of Science and Technology --- .github/workflows/main.yml | 2 +- README.md | 1 + conf/oist.config | 22 ++++++++++++++++++++++ docs/oist.md | 33 +++++++++++++++++++++++++++++++++ nfcore_custom.config | 1 + 5 files changed, 58 insertions(+), 1 deletion(-) create mode 100644 conf/oist.config create mode 100644 docs/oist.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index ea2117d..3e5c930 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', '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', '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/README.md b/README.md index a590599..45721e8 100644 --- a/README.md +++ b/README.md @@ -116,6 +116,7 @@ Currently documentation is available for the following systems: * [KRAKEN](docs/kraken.md) * [MPCDF](docs/mpcdf.md) * [MUNIN](docs/munin.md) +* [OIST](docs/oist.md) * [PASTEUR](docs/pasteur.md) * [PHOENIX](docs/phoenix.md) * [PRINCE](docs/prince.md) diff --git a/conf/oist.config b/conf/oist.config new file mode 100644 index 0000000..8815ed4 --- /dev/null +++ b/conf/oist.config @@ -0,0 +1,22 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'The Okinawa Institute of Science and Technology Graduate University (OIST) HPC cluster profile provided by nf-core/configs.' + config_profile_contact = 'OISTs Bioinformatics User Group ' + config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/oist.md' +} + +singularity { + enabled = true +} + +process { + executor = 'slurm' + queue = 'compute' + clusterOptions = '-C zen2' +} + +params { + max_memory = 500.GB + max_cpus = 128 + max_time = 90.h +} diff --git a/docs/oist.md b/docs/oist.md new file mode 100644 index 0000000..8c4a68c --- /dev/null +++ b/docs/oist.md @@ -0,0 +1,33 @@ +# nf-core/configs: OIST Configuration + +The nf-core pipelines [rnaseq](https://nf-co.re/rnaseq) and +[eager](https://nf-co.re/eager) have been successfully tested on the _Deigo_ +cluster at the Okinawa Institute of Science and Technology Graduate University +([OIST](https://www.oist.jp)). We have no reason to expect that other +pipelines would not work. + +To use, run the pipeline with `-profile oist`. This will download and launch +the [`oist.config`](../conf/oist.config) which has been pre-configured with a +setup suitable for _Deigo_. 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. + +## Below are non-mandatory information e.g. on modules to load etc + +Before running the pipeline you will need to load Nextflow and Singularity +using the environment module system on _Deigo_. You can do this by issuing the +commands below: + +```bash +## Load the latest Nextflow and Singularity environment modules +ml purge +ml bioinfo-ugrp-modules +ml Other/Nextflow +``` + +>NB: You will need an account to use the _Deigo_ cluster in order to run the +>pipeline. If in doubt contact IT. +> +>NB: Nextflow will submit the jobs via the SLURM scheduler to the HPC cluster +>and as such the commands above will have to be executed on one of the login +>nodes. If in doubt contact IT. diff --git a/nfcore_custom.config b/nfcore_custom.config index 7310de5..429e3c1 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -35,6 +35,7 @@ profiles { kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" } mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" } munin { includeConfig "${params.custom_config_base}/conf/munin.config" } + oist { includeConfig "${params.custom_config_base}/conf/oist.config" } pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" }