Now added user.home property to JAVA_OPTIONS

Plant-Food-Research-Open · Nov 5, 2024 · 0f9a4ee · 0f9a4ee
1 parent e6b968f
commit 0f9a4ee
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/modules/local/runassemblyvisualizer.nf b/modules/local/runassemblyvisualizer.nf
@@ -21,7 +21,8 @@ process RUNASSEMBLYVISUALIZER {
     assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g')
     file_name="${agp_assembly_file}"
 
-    export _JAVA_OPTIONS="-Djava.util.prefs.userRoot=user_prefs -Xms${avail_mem}g -Xmx${avail_mem}g"
+    mkdir user_home
+    export _JAVA_OPTIONS="-Djava.util.prefs.userRoot=user_prefs -Duser.home=user_home -Xms${avail_mem}g -Xmx${avail_mem}g"
 
     /usr/src/3d-dna/visualize/run-assembly-visualizer.sh \\
         -p false \\