diff --git a/docs/vsc_ugent.md b/docs/vsc_ugent.md index 5dd38b39..cea1f8a9 100644 --- a/docs/vsc_ugent.md +++ b/docs/vsc_ugent.md @@ -5,7 +5,8 @@ > [!IMPORTANT] > You will need an [account](https://www.ugent.be/hpc/en/access/faq/access) to use the HPC cluster to run the pipeline. -Regarding environment variables in `~/.bashrc`, make sure you have a setup similar to the one below. If you're already part of a VO, ask for one or use `VSC_DATA_USER` instead of `VSC_DATA_VO_USER`. +Make sure you have an environment variable setup similar to the one below in `~/.bashrc`. If you're not already part of a VO, ask your admin to add you or use `VSC_DATA_USER` instead of `VSC_DATA_VO_USER`. +For more installation help, read the documentation of a Nextflow workshop on VSC infrastructure like [this one](https://vibbits-nextflow-workshop.readthedocs.io/en/latest/installations.html). ```bash # Needed for Tier1 accounts, not for Tier2 @@ -15,8 +16,8 @@ export SBATCH_ACCOUNT=$SLURM_ACCOUNT # Needed for running Nextflow jobs export NXF_HOME=$VSC_DATA_VO_USER/.nextflow # Needed for running Apptainer containers -export APPTAINER_CACHEDIR=$VSC_DATA_VO_USER/.apptainer/cache -export APPTAINER_TMPDIR=$VSC_DATA_VO_USER/.apptainer/tmp +export APPTAINER_CACHEDIR=$VSC_SCRATCH_VO_USER/.apptainer/cache +export APPTAINER_TMPDIR=$VSC_SCRATCH_VO_USER/.apptainer/tmp ``` First you should go to the cluster you want to run the pipeline on. You can check what clusters have the most free space on this [link](https://shieldon.ugent.be:8083/pbsmon-web-users/). Use the following commands to easily switch between clusters: @@ -55,8 +56,11 @@ qsub