fix: Only --bind Snakemake when we're working with a Python script (#…

…1206)

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

snakemake/deployment/singularity.py

@@ -113,6 +113,7 @@ def shellcmd(
     envvars=None,
     shell_executable=None,
     container_workdir=None,
+    is_python_script=False,
 ):
     """Execute shell command inside singularity container given optional args
     and environment variables to be passed."""
@@ -131,8 +132,9 @@ def shellcmd(
         # because we cannot be sure where it is located in the container.
         shell_executable = os.path.split(shell_executable)[-1]
 
-    # mount host snakemake module into container
-    args += " --bind {}:{}".format(SNAKEMAKE_SEARCHPATH, SNAKEMAKE_MOUNTPOINT)
+    if is_python_script:
+        # mount host snakemake module into container
+        args += " --bind {}:{}".format(SNAKEMAKE_SEARCHPATH, SNAKEMAKE_MOUNTPOINT)
 
     if container_workdir:
         args += " --pwd {}".format(container_workdir)

snakemake/script.py

@@ -579,7 +579,9 @@ def execute_script(self, fname, edit=False):
             # bash is configured as executable on Windows
             py_exec = py_exec.replace("\\", "/")
         # use the same Python as the running process or the one from the environment
-        self._execute_cmd("{py_exec} {fname:q}", py_exec=py_exec, fname=fname)
+        self._execute_cmd(
+            "{py_exec} {fname:q}", py_exec=py_exec, fname=fname, is_python_script=True
+        )
 
 
 class RScript(ScriptBase):

snakemake/shell.py

@@ -184,6 +184,7 @@ def __new__(
                 envvars=None,
                 shell_executable=cls._process_args["executable"],
                 container_workdir=shadow_dir,
+                is_python_script=context.get("is_python_script", False),
             )
             logger.info("Activating singularity image {}".format(container_img))
         if conda_env: