quote singularity env parameters

destination parameters that contain spaces, e.g. ``` <param id="singularity_env__JAVA_OPTIONS">-Xmx61g -Xms256m</param> ``` need quoting.
bgruening · Nov 20, 2023 · a0f0b83 · a0f0b83
1 parent 74ef0d8
commit a0f0b83
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/lib/galaxy/tool_util/deps/singularity_util.py b/lib/galaxy/tool_util/deps/singularity_util.py
@@ -81,7 +81,7 @@ def build_singularity_run_command(
     for key, value in env:
         if key == "HOME":
             home = value
-        command_parts.extend([f"SINGULARITYENV_{key}={value}"])
+        command_parts.extend([f'SINGULARITYENV_{key}="{value}"'])
     command_parts += _singularity_prefix(
         singularity_cmd=singularity_cmd,
         sudo=sudo,