Merge pull request #203 from oist/draftOISTconfig

Institutional profile for the Okinawa Institute of Science and Technology (OIST)

.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

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)

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 <BioinfoUgrp@oist.jp>'
+  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
+}

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.

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" }