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modify alternative module load

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qlr900 2022-07-06 12:54:07 +02:00
parent 7ac08a1015
commit 8a781b6bb2
1 changed files with 4 additions and 2 deletions
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docs/ku_sund_dangpu.md
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@ -13,7 +13,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using
## Load Nextflow and Singularity environment modules ## Load Nextflow and Singularity environment modules
module purge module purge
module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0
# alternative module load jdk/1.8.0_291 nextflow/22.04.3 singularity/3.8.0 # alternative module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0
export NXF_OPTS='-Xms1g -Xmx4g' export NXF_OPTS='-Xms1g -Xmx4g'
export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home
export NXF_TEMP=/scratch/tmp export NXF_TEMP=/scratch/tmp
@ -26,7 +26,9 @@ mkdir $NXF_SINGULARITY_CACHEDIR
mkdir $NXF_HOME mkdir $NXF_HOME
``` ```
finally download and test the pipeline of choice using the `-profile ku_sund_dangpu` Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm as resource manager within the ku_sund_dangpu profile. Just make sure that the pipeline is run within a tmux session.
``` ```
nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
``` ```