Merge pull request #14470 from mvdbeek/singularity_fix_cleanenv

[22.05] Fix position of cleanenv flag in singularity command

lib/galaxy/tool_util/deps/singularity_util.py

@@ -75,10 +75,10 @@ def build_singularity_run_command(
         sudo=sudo,
         sudo_cmd=sudo_cmd,
     )
-    if cleanenv:
-        command_parts.append("--cleanenv")
     command_parts.append("-s")
     command_parts.append("exec")
+    if cleanenv:
+        command_parts.append("--cleanenv")
     for volume in volumes:
         command_parts.extend(["-B", str(volume)])
     if home is not None:

test/unit/tool_util/test_singularity_util.py

@@ -0,0 +1,18 @@
+from galaxy.tool_util.deps.singularity_util import build_singularity_run_command
+
+
+def test_build_singularity_run_command_defaults():
+    cmd = build_singularity_run_command(
+        container_command="echo hi",
+        image="busybox",
+    )
+    assert cmd == "singularity -s exec --cleanenv busybox echo hi"
+
+
+def test_build_singularity_run_command_no_cleanenv():
+    cmd = build_singularity_run_command(
+        container_command="echo hi",
+        image="busybox",
+        cleanenv=False,
+    )
+    assert cmd == "singularity -s exec busybox echo hi"