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41 lines
2.2 KiB
Markdown
41 lines
2.2 KiB
Markdown
# nf-core/configs: University of Ghent High Performance Computing Infrastructure (VSC)
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> **NB:** You will need an [account](https://www.ugent.be/hpc/en/access/faq/access) to use the HPC cluster to run the pipeline.
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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:
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```shell
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module purge
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module swap cluster/<CLUSTER>
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```
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Before running the pipeline you will need to create a SLURM/PBS script to submit as a job.
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```bash
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#!/bin/bash
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module load Nextflow
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nextflow run <pipeline> -profile vsc_ugent,<CLUSTER> <Add your other parameters>
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```
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I also highly recommend specifying a location of a Singularity cache directory, by specifying the location with the `$SINGULARITY_CACHEDIR` bash environment variable in your `.bash_profile` or `.bashrc` or by adding it to your SLURM/PBS script. If this cache directory is not specified, the cache directory defaults to your `$HOME/.singularity` directory, which does not have a lot of disk space.
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```shell
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export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity
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```
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All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
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The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space.
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You can also add several TORQUE options to the SLURM/PBS script. More about this on this [link](http://hpcugent.github.io/vsc_user_docs/pdf/intro-HPC-linux-gent.pdf#appendix.B).
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To submit your job to the cluster by using the following command:
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```shell
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qsub <script name>.pbs
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```
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> **NB:** The profile only works for the clusters `skitty`, `swalot`, `victini`, `kirlia` and `doduo`.
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> **NB:** The default directory where the `work/` and `singularity` (cache directory for images) is located in `$VSC_SCRATCH_VO_USER`.
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