fix: respect shebang lines in post-deploy scripts (see deployment doc…

…s) (#1841)

* fix: use configured shell executable for post deploy scripts

* Note on default shell.

* Use shebang for post-deploy script execution

docs/snakefiles/deployment.rst

@@ -353,7 +353,15 @@ Post-deployment scripts must be placed next to their corresponding environment-f
         └── interproscan.post-deploy.sh
 
 The path of the conda environment can be accessed within the script via ``$CONDA_PREFIX``.
+Importantly, if the script relies on certain shell specific syntax, (e.g. `set -o pipefail` for bash), make sure to add a matching shebang to the script, e.g.:
 
+.. code-block:: bash
+
+    #!env bash
+    set -o pipefail
+    # ...
+
+If no shebang line like above (``#!env bash``) is provided, the script will be executed with the ``sh`` command.
 
 .. _conda_named_env:
 

docs/snakefiles/rules.rst

@@ -27,6 +27,7 @@ Inside the shell command, all local and global variables, especially input and o
 Here, input and output (and in general any list or tuple) automatically evaluate to a space-separated list of files (i.e. ``path/to/inputfile path/to/other/inputfile``).
 From Snakemake 3.8.0 on, adding the special formatting instruction ``:q`` (e.g. ``"somecommand {input:q} {output:q}")``) will let Snakemake quote each of the list or tuple elements that contains whitespace.
 
+By default shell commands will be invoked with ``bash`` shell (unless the workflow specifies a different default shell via ``shell.executable(...)``).
 
 Instead of a shell command, a rule can run some python code to generate the output:
 

snakemake/deployment/conda.py

@@ -350,8 +350,16 @@ def execute_deployment_script(self, env_file, deploy_file):
                 os.path.relpath(path=deploy_file, start=os.getcwd())
             )
         )
+
+        # Determine interpreter from shebang or use sh as default.
+        interpreter = "sh"
+        with open(deploy_file, "r") as f:
+            first_line = next(iter(f))
+            if first_line.startswith("#!"):
+                interpreter = first_line[2:].strip()
+
         shell.check_output(
-            self.conda.shellcmd(self.address, "sh {}".format(deploy_file)),
+            self.conda.shellcmd(self.address, f"{interpreter} {deploy_file}"),
             stderr=subprocess.STDOUT,
         )
 

test.sh

@@ -0,0 +1,5 @@
+set -o pipefail
+
+echo $BASH
+
+echo test