Merge pull request #376 from nvnieuwk/vsc_ugent

Added the VSC UGent profile

.github/workflows/main.yml

@@ -86,6 +86,7 @@ jobs:
           - "utd_sysbio"
           - "uzh"
           - "vai"
+          - "vsc_ugent"
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -139,6 +139,7 @@ Currently documentation is available for the following systems:
 - [UTD_SYSBIO](docs/utd_sysbio.md)
 - [UZH](docs/uzh.md)
 - [VAI](docs/vai.md)
+- [VSC_UGENT](docs/vsc_ugent.md)
 
 ### Uploading to `nf-core/configs`
 

conf/vsc_ugent.config

@@ -0,0 +1,115 @@
+// Specify the work directory
+workDir = "$VSC_SCRATCH_VO_USER/work"
+
+// Perform work directory cleanup when the run has succesfully completed
+cleanup = true
+
+// Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
+executor {
+    submitRateLimit = '10 sec'
+}
+
+// Specify that singularity should be used and where the cache dir will be for the images
+singularity {
+    enabled = true
+    autoMounts = true
+    cacheDir = "$VSC_SCRATCH_VO_USER/singularity"
+}
+
+// Define profiles for each cluster
+profiles {
+    skitty {
+        params {
+            config_profile_description = 'HPC_SKITTY profile for use on the Skitty cluster of the VSC HPC.'
+            config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
+            config_profile_url = 'https://www.ugent.be/hpc/en'
+            max_memory = 177.GB
+            max_cpus = 36
+            max_time = 72.h
+        }
+
+        process {
+            executor = 'slurm'
+            queue = 'skitty'
+            maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
+            scratch = "$VSC_SCRATCH_VO_USER"
+        }
+    }
+
+    swalot {
+        params {
+            config_profile_description = 'HPC_SWALOT profile for use on the Swalot cluster of the VSC HPC.'
+            config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
+            config_profile_url = 'https://www.ugent.be/hpc/en'
+            max_memory = 116.GB
+            max_cpus = 20
+            max_time = 72.h
+        }
+
+        process {
+            executor = 'slurm'
+            queue = 'swalot'
+            maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
+            scratch = "$VSC_SCRATCH_VO_USER"
+        }
+    }
+
+    victini {
+        params {
+            config_profile_description = 'HPC_VICTINI profile for use on the Victini cluster of the VSC HPC.'
+            config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
+            config_profile_url = 'https://www.ugent.be/hpc/en'
+            max_memory = 88.GB
+            max_cpus = 36
+            max_time = 72.h
+        }
+
+        process {
+            executor = 'slurm'
+            queue = 'victini'
+            maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
+            scratch = "$VSC_SCRATCH_VO_USER"
+        }
+    }
+
+    kirlia {
+        params {
+            config_profile_description = 'HPC_KIRLIA profile for use on the Kirlia cluster of the VSC HPC.'
+            config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
+            config_profile_url = 'https://www.ugent.be/hpc/en'
+            max_memory = 738.GB
+            max_cpus = 36
+            max_time = 72.h
+        }
+
+        process {
+            executor = 'slurm'
+            queue = 'kirlia'
+            maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
+            scratch = "$VSC_SCRATCH_VO_USER"
+        }
+    }
+
+    doduo {
+        params {
+            config_profile_description = 'HPC_DODUO profile for use on the Doduo cluster of the VSC HPC.'
+            config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
+            config_profile_url = 'https://www.ugent.be/hpc/en'
+            max_memory = 250.GB
+            max_cpus = 96
+            max_time = 72.h
+        }
+
+        process {
+            executor = 'slurm'
+            queue = 'doduo'
+            maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
+            scratch = "$VSC_SCRATCH_VO_USER"
+        }
+    }
+}

docs/vsc_ugent.md

@@ -0,0 +1,37 @@
+# nf-core/configs: University of Ghent High Performance Computing Infrastructure (VSC)
+
+> **NB:** You will need an [account](https://www.ugent.be/hpc/en/access/faq/access) to use the HPC cluster to run the pipeline.
+
+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:
+
+```shell
+module purge
+module swap cluster/<CLUSTER>
+```
+
+Before running the pipeline you will need to create a PBS script to submit as a job.
+
+```bash
+#!/bin/bash
+
+module load Nextflow
+
+nextflow run <pipeline> -profile vsc_ugent,<CLUSTER> <Add your other parameters>
+```
+
+I also highly recommend specifying a location of a Singularity cache directory, by specifying the location with the `$SINGULARITY_CACHEDIR` bash environment variable in your `.bash_profile` or `.bashrc` or by adding it to your PBS script. If this cache directory is not specified,
+
+All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
+The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. The default work directory is set to `$VSC_SCRATCH_VO_USER/work` per this configuration
+
+You can also add several TORQUE options to the PBS script. More about this on this [link](http://hpcugent.github.io/vsc_user_docs/pdf/intro-HPC-linux-gent.pdf#appendix.B).
+
+To submit your job to the cluster by using the following command:
+
+```shell
+qsub <script name>.pbs
+```
+
+> **NB:** The profile only works for the clusters `skitty`, `swalot`, `victini`, `kirlia` and `doduo`.
+
+> **NB:** The default directory where the `work/` and `singularity/` (cache directory for images) is located in `$VSC_SCRATCH_VO_USER`.

nfcore_custom.config

@@ -68,4 +68,5 @@ profiles {
   utd_sysbio   { includeConfig "${params.custom_config_base}/conf/utd_sysbio.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }
   vai          { includeConfig "${params.custom_config_base}/conf/vai.config" }
+  vsc_ugent    { includeConfig "${params.custom_config_base}/conf/vsc_ugent.config" }
 }