improve tmpDir handling

icbi-lab · Sep 29, 2021 · 50006c7 · 50006c7
1 parent b4000c9
commit 50006c7
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Showing 3 changed files with 80 additions and 74 deletions.
diff --git a/conf/params.config b/conf/params.config
@@ -269,6 +269,7 @@ manifest {
 //
 import java.nio.file.Paths;
 
+new File(params.tmpDir).mkdirs()
 params.singularityTmpMount = params.tmpDir.startsWith("/tmp/") ? "/tmp" : Paths.get(params.tmpDir).toRealPath()
 params.singularityHLAHDmount = (params.HLAHD_DIR != "") ? " -B " + Paths.get(params.HLAHD_DIR).toRealPath() : ""
 params.singularityAssetsMount = projectDir.toRealPath() + "/assets"

diff --git a/conf/params_icbi.config b/conf/params_icbi.config
@@ -265,7 +265,8 @@ manifest {
 //
 import java.nio.file.Paths;
 
-params.singularityTmpMount = params.tmpDir.startsWith("/tmp") ? "/tmp" : Paths.get(params.tmpDir).toRealPath()
+new File(params.tmpDir).mkdirs()
+params.singularityTmpMount = params.tmpDir.startsWith("/tmp/") ? "/tmp" : Paths.get(params.tmpDir).toRealPath()
 params.singularityHLAHDmount = (params.HLAHD_DIR != "") ? " -B " + Paths.get(params.HLAHD_DIR).toRealPath() : ""
 params.singularityAssetsMount = projectDir.toRealPath() + "/assets"