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34 lines
1.3 KiB
Markdown
34 lines
1.3 KiB
Markdown
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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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