From b22e8b79c7f233918fef4a8f637376fc1d946144 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 1 Sep 2022 11:01:23 +0200
Subject: [PATCH] Fix cheaha config due to use of environmental variable

---
 conf/cheaha.config | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/conf/cheaha.config b/conf/cheaha.config
index 578259c..58963b5 100644
--- a/conf/cheaha.config
+++ b/conf/cheaha.config
@@ -1,3 +1,6 @@
+// Define the Scratch directory
+def scratch_dir = System.getenv("USER_SCRATCH") ?: "/tmp"
+
 params {
     config_profile_name = 'cheaha'
     config_profile_description = 'University of Alabama at Birmingham Cheaha HPC'
@@ -6,14 +9,14 @@ params {
 }
 
 env {
-    TMPDIR="$USER_SCRATCH"
-    SINGULARITY_TMPDIR="$USER_SCRATCH"
+    TMPDIR="$USER"
+    SINGULARITY_TMPDIR="$scratch_dir"
 }
 
 singularity {
     enabled = true
     autoMounts = true
-    runOptions = "--contain --workdir $USER_SCRATCH"
+    runOptions = "--contain --workdir $scratch_dir"
 }
 
 process {