From 44e25830e46da3cad3873b2e9fc8be3b6d1eaad3 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 7 Jun 2022 11:33:22 +0200
Subject: [PATCH] update for vsc_ugent

---
 conf/vsc_ugent.config | 29 ++++++++++++++++-------------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/conf/vsc_ugent.config b/conf/vsc_ugent.config
index 560367a..f2558fc 100644
--- a/conf/vsc_ugent.config
+++ b/conf/vsc_ugent.config
@@ -1,8 +1,11 @@
+// Define the Scratch directory
+def scratch_dir = System.getenv("VSC_SCRATCH_VO_USER") ?: "scratch/"
+
 // Specify the work directory
-workDir = "$VSC_SCRATCH_VO_USER/work"
+workDir = "$scratch_dir/work"
 
 // Perform work directory cleanup when the run has succesfully completed
-cleanup = true
+// cleanup = true
 
 // Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
 executor {
@@ -13,7 +16,7 @@ executor {
 singularity {
     enabled = true
     autoMounts = true
-    cacheDir = "$VSC_SCRATCH_VO_USER/singularity"
+    cacheDir = "$scratch_dir/singularity"
 }
 
 // Define profiles for each cluster
@@ -32,8 +35,8 @@ profiles {
             executor = 'slurm'
             queue = 'skitty'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 
@@ -51,8 +54,8 @@ profiles {
             executor = 'slurm'
             queue = 'swalot'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 
@@ -70,8 +73,8 @@ profiles {
             executor = 'slurm'
             queue = 'victini'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 
@@ -89,8 +92,8 @@ profiles {
             executor = 'slurm'
             queue = 'kirlia'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 
@@ -108,8 +111,8 @@ profiles {
             executor = 'slurm'
             queue = 'doduo'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 }
\ No newline at end of file