diff --git a/conf/computerome.config b/conf/computerome.config index b42cbf353..480e44104 100644 --- a/conf/computerome.config +++ b/conf/computerome.config @@ -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" diff --git a/docs/computerome.md b/docs/computerome.md index b2e624f0e..ef3578f66 100644 --- a/docs/computerome.md +++ b/docs/computerome.md @@ -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/` 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/` 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.