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Institutional profile for Okinawa Institute of Science and Technology
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2
.github/workflows/main.yml
vendored
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.github/workflows/main.yml
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@ -16,7 +16,7 @@ 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: ['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']
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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']
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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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@ -116,6 +116,7 @@ Currently documentation is available for the following systems:
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* [KRAKEN](docs/kraken.md)
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* [KRAKEN](docs/kraken.md)
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* [MPCDF](docs/mpcdf.md)
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* [MPCDF](docs/mpcdf.md)
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* [MUNIN](docs/munin.md)
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* [MUNIN](docs/munin.md)
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* [OIST](docs/oist.md)
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* [PASTEUR](docs/pasteur.md)
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* [PASTEUR](docs/pasteur.md)
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* [PHOENIX](docs/phoenix.md)
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* [PHOENIX](docs/phoenix.md)
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* [PRINCE](docs/prince.md)
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* [PRINCE](docs/prince.md)
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22
conf/oist.config
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conf/oist.config
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@ -0,0 +1,22 @@
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//Profile config names for nf-core/configs
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params {
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config_profile_description = 'The Okinawa Institute of Science and Technology Graduate University (OIST) HPC cluster profile provided by nf-core/configs.'
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config_profile_contact = 'OISTs Bioinformatics User Group <BioinfoUgrp@oist.jp>'
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config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/oist.md'
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}
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singularity {
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enabled = true
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}
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process {
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executor = 'slurm'
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queue = 'compute'
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clusterOptions = '-C zen2'
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}
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params {
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max_memory = 500.GB
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max_cpus = 128
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max_time = 90.h
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}
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docs/oist.md
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docs/oist.md
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@ -0,0 +1,33 @@
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# nf-core/configs: OIST Configuration
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The nf-core pipelines [rnaseq](https://nf-co.re/rnaseq) and
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[eager](https://nf-co.re/eager) have been successfully tested on the _Deigo_
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cluster at the Okinawa Institute of Science and Technology Graduate University
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([OIST](https://www.oist.jp)). We have no reason to expect that other
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pipelines would not work.
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To use, run the pipeline with `-profile oist`. This will download and launch
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the [`oist.config`](../conf/oist.config) which has been pre-configured with a
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setup suitable for _Deigo_. Using this profile, a docker image containing all
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of the required software will be downloaded, and converted to a Singularity
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image before execution of the pipeline.
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## Below are non-mandatory information e.g. on modules to load etc
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Before running the pipeline you will need to load Nextflow and Singularity
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using the environment module system on _Deigo_. You can do this by issuing the
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commands below:
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```bash
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## Load the latest Nextflow and Singularity environment modules
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ml purge
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ml bioinfo-ugrp-modules
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ml Other/Nextflow
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```
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>NB: You will need an account to use the _Deigo_ cluster in order to run the
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>pipeline. If in doubt contact IT.
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>
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>NB: Nextflow will submit the jobs via the SLURM scheduler to the HPC cluster
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>and as such the commands above will have to be executed on one of the login
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>nodes. If in doubt contact IT.
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@ -35,6 +35,7 @@ profiles {
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kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" }
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kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" }
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mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
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mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
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munin { includeConfig "${params.custom_config_base}/conf/munin.config" }
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munin { includeConfig "${params.custom_config_base}/conf/munin.config" }
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oist { includeConfig "${params.custom_config_base}/conf/oist.config" }
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pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
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pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
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phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
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phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
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prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
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prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
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