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Update computerome docs to latest module requiremetns #685

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Update computerome docs to latest module requiremetns #685

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903eb8b
Updated module reuqiremetns
jfy133 May 15, 2024
82aaa62
Update singularity version
jfy133 May 15, 2024
9722f3f
Fix linting I hope
jfy133 May 15, 2024
e4cd137
Merge branch 'master' into computerome-docs
AdrijaK Jun 3, 2024
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2 changes: 1 addition & 1 deletion conf/computerome.config
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Expand Up @@ -23,7 +23,7 @@ singularity {
}

process {
beforeScript = "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=$params.cache_dir"
beforeScript = "module load tools singularity/4.0.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=$params.cache_dir"
executor = 'pbs'
queueSize = 2000
clusterOptions = "-A $params.project -W group_list=$params.project"
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2 changes: 1 addition & 1 deletion docs/computerome.md
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Expand Up @@ -4,7 +4,7 @@ To use, run the pipeline with `-profile computerome`. This will download and lau

## Using the Computerome config profile

Before running the pipeline you will need to load `Nextflow` using the environment module system (this can be done with e.g. `module load tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
Before running the pipeline you will need to load `Nextflow` using the environment module system (this can be done with e.g. `module load tools jdk/19 singularity/4.0.0 nextflow/<VERSION>` where `VERSION` is e.g. `23.04.3`).

To use, run the pipeline with `-profile computerome` (one hyphen).
This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome servers.
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