From 7cff7b47af9274714d7fb0ce27a72f78d43ba5ef Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 5 Aug 2024 11:10:30 +0200
Subject: [PATCH] Remove erroneous mount home functionality

This should be determined by the tool profile
---
 lib/galaxy/config/sample/job_conf.xml.sample_advanced | 6 ------
 lib/galaxy/tool_util/deps/container_classes.py        | 1 -
 lib/galaxy/tool_util/deps/singularity_util.py         | 7 +++----
 3 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
index b91f6e5425a7..0ae9c855d3be 100644
--- a/lib/galaxy/config/sample/job_conf.xml.sample_advanced
+++ b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -647,12 +647,6 @@
                singularity_ipc to `false`.
           -->
           <!-- <param id="singularity_ipc">true</param> -->
-          <!-- Singularity mounts $HOME by default. This can be problematic if home
-               contains sensitive data, is shared across nodes or has configuration
-               files affecting reproducibility. Therefore Galaxy passes the `contain`
-               argument to isolate $HOME. If $HOME must be mounted, it can be
-               turned on by setting singularity_mount_home to `true`. -->
-          <!-- <param id="singularity_mount_home">false</param> -->
           <!-- Pass extra arguments to the singularity exec command not covered by the
                above options. -->
           <!-- <param id="singularity_run_extra_arguments"></param> -->
diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py
index 55acaae81b86..e00c005e5275 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)),
-            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 1eee5abdb74f..cd4d69161a54 100644
--- a/lib/galaxy/tool_util/deps/singularity_util.py
+++ b/lib/galaxy/tool_util/deps/singularity_util.py
@@ -83,7 +83,6 @@ def build_singularity_run_command(
     cleanenv: bool = DEFAULT_CLEANENV,
     ipc: bool = DEFAULT_IPC,
     pid: bool = DEFAULT_PID,
-    mount_home: bool = DEFAULT_MOUNT_HOME,
     no_mount: Optional[List[str]] = DEFAULT_NO_MOUNT,
 ) -> str:
     volumes = volumes or []
@@ -104,8 +103,8 @@ def build_singularity_run_command(
     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.
+    # requested volumes to be mounted. This gives fully full-control over
+    # the mounting behavior.
     command_parts.append("--contain")
     if working_directory:
         command_parts.extend(["--pwd", working_directory])
@@ -119,7 +118,7 @@ def build_singularity_run_command(
         command_parts.extend(["--no-mount", ",".join(no_mount)])
     for volume in volumes:
         command_parts.extend(["-B", str(volume)])
-    if mount_home and home is not None:
+    if home is not None:
         command_parts.extend(["--home", f"{home}:{home}"])
     if run_extra_arguments:
         command_parts.append(run_extra_arguments)