From c2b26a734dab21d92d0d2dd45ca58aeb31296301 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 20 May 2022 09:48:19 +0200
Subject: [PATCH] automated the internal cache dir location for singularity

---
 conf/vsc_ugent.config |  5 +++++
 docs/vsc_ugent.md     | 10 +++-------
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/conf/vsc_ugent.config b/conf/vsc_ugent.config
index 7df41f9..560367a 100644
--- a/conf/vsc_ugent.config
+++ b/conf/vsc_ugent.config
@@ -32,6 +32,7 @@ profiles {
             executor = 'slurm'
             queue = 'skitty'
             maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
             scratch = "$VSC_SCRATCH_VO_USER"
         }
     }
@@ -50,6 +51,7 @@ profiles {
             executor = 'slurm'
             queue = 'swalot'
             maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
             scratch = "$VSC_SCRATCH_VO_USER"
         }
     }
@@ -68,6 +70,7 @@ profiles {
             executor = 'slurm'
             queue = 'victini'
             maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
             scratch = "$VSC_SCRATCH_VO_USER"
         }
     }
@@ -86,6 +89,7 @@ profiles {
             executor = 'slurm'
             queue = 'kirlia'
             maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
             scratch = "$VSC_SCRATCH_VO_USER"
         }
     }
@@ -104,6 +108,7 @@ profiles {
             executor = 'slurm'
             queue = 'doduo'
             maxRetries = 2
+            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
             scratch = "$VSC_SCRATCH_VO_USER"
         }
     }
diff --git a/docs/vsc_ugent.md b/docs/vsc_ugent.md
index 95c7f96..027e123 100644
--- a/docs/vsc_ugent.md
+++ b/docs/vsc_ugent.md
@@ -19,16 +19,12 @@ 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 `$SINGULARITY_CACHEDIR` bash environment variable in your `.bash_profile` or `.bashrc` or by adding it to your SLURM/PBS script. If this cache directory is not specified, the cache directory defaults to your `$HOME/.singularity` directory, which does not have a lot of disk space.
-
-```shell
-export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity
-```
+I also highly recommend specifying a location of a Singularity cache directory, by specifying the location with the `$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).
+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).
 
 To submit your job to the cluster by using the following command:
 
@@ -38,4 +34,4 @@ 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 `$VSC_SCRATCH_VO_USER`.
+> **NB:** The default directory where the `work/` and `singularity/` (cache directory for images) is located in `$VSC_SCRATCH_VO_USER`.