From 74e5612742060bd28b75d7ff5aa9b4c55bb0b4ec Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 31 Jul 2024 09:11:43 +0200
Subject: [PATCH] Remove redundant --contain switch

---
 lib/galaxy/tool_util/deps/container_classes.py | 1 -
 lib/galaxy/tool_util/deps/singularity_util.py  | 9 +++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py
index 8891c95af830..55acaae81b86 100644
--- a/lib/galaxy/tool_util/deps/container_classes.py
+++ b/lib/galaxy/tool_util/deps/container_classes.py
@@ -575,7 +575,6 @@ def containerize_command(self, command: str) -> str:
             cleanenv=asbool(self.prop("cleanenv", singularity_util.DEFAULT_CLEANENV)),
             ipc=asbool(self.prop("ipc", singularity_util.DEFAULT_IPC)),
             pid=asbool(self.prop("pid", singularity_util.DEFAULT_PID)),
-            contain=asbool(self.prop("contain", singularity_util.DEFAULT_CONTAIN)),
             mount_home=asbool(self.prop("mount_home", singularity_util.DEFAULT_MOUNT_HOME)),
             no_mount=self.prop("no_mount", singularity_util.DEFAULT_NO_MOUNT),
             **self.get_singularity_target_kwds(),
diff --git a/lib/galaxy/tool_util/deps/singularity_util.py b/lib/galaxy/tool_util/deps/singularity_util.py
index ebeb9922329e..1eee5abdb74f 100644
--- a/lib/galaxy/tool_util/deps/singularity_util.py
+++ b/lib/galaxy/tool_util/deps/singularity_util.py
@@ -21,7 +21,6 @@
 # the ipc namespace, this fixes some issues with python multiprocessing.
 # --cleanenv makes sure the current environment is not inherited.
 DEFAULT_CLEANENV = True
-DEFAULT_CONTAIN = True
 DEFAULT_IPC = True
 DEFAULT_PID = True
 DEFAULT_MOUNT_HOME = False
@@ -84,7 +83,6 @@ def build_singularity_run_command(
     cleanenv: bool = DEFAULT_CLEANENV,
     ipc: bool = DEFAULT_IPC,
     pid: bool = DEFAULT_PID,
-    contain: bool = DEFAULT_CONTAIN,
     mount_home: bool = DEFAULT_MOUNT_HOME,
     no_mount: Optional[List[str]] = DEFAULT_NO_MOUNT,
 ) -> str:
@@ -104,6 +102,11 @@ def build_singularity_run_command(
     )
     command_parts.append("-s")
     command_parts.append("exec")
+    # Singularity mounts some directories, such as $HOME and $PWD by default.
+    # using --contain disables this behaviour and only allows explicitly
+    # requested volumes to be mounted. Since galaxy already mounts $PWD and
+    # mount_home can be activated, a switch for --contain is redundant.
+    command_parts.append("--contain")
     if working_directory:
         command_parts.extend(["--pwd", working_directory])
     if cleanenv:
@@ -112,8 +115,6 @@ def build_singularity_run_command(
         command_parts.append("--ipc")
     if pid:
         command_parts.append("--pid")
-    if contain:
-        command_parts.append("--contain")
     if no_mount:
         command_parts.extend(["--no-mount", ",".join(no_mount)])
     for volume in volumes: