feat: support for post deploy scripts

docs/snakefiles/deployment.rst

@@ -262,6 +262,30 @@ Conda deployment also works well for offline or air-gapped environments. Running
 
 .. _singularity:
 
+
+-------------------------
+Providing post-deployment scripts
+-------------------------
+
+With Snakemake 9.14 post-deployment shell-scripts can be provided to perform additional adjustments of a conda environment.
+This might be helpful in case a conda package is missing components or requires further configuration for execution.
+post-deployment scripts must be placed next to their corresponding environment-file and require the suffix ``.post-deploy.sh``.
+
+.. code-block:: python
+
+    rule NAME:
+        input:
+            "seqs.fastq"
+        output:
+            "results.tsv"
+        conda:
+            "envs/interproscan.yaml"
+            "envs/interproscan.post-deploy.sh
+        shell:
+            "interproscan.sh -i {input} -f tsv -o {output}"
+
+The path of the conda environment can be accessed within the script via ``$CONDA_PREFIX``.
+
 --------------------------
 Running jobs in containers
 --------------------------

snakemake/deployment/conda.py

@@ -4,6 +4,7 @@
 __license__ = "MIT"
 
 import os
+from pathlib import Path
 import re
 from snakemake.sourcecache import LocalGitFile, LocalSourceFile, infer_source_file
 import subprocess
@@ -211,6 +212,29 @@ def create_archive(self):
             raise e
         return env_archive
 
+    def execute_deployment_script(self, env_file):
+        """Execute post-deployment script if present"""
+        from snakemake.shell import shell
+
+        post_deploy_script = Path(env_file).with_suffix(".post-deploy.sh")
+        if post_deploy_script.exists():
+            if ON_WINDOWS:
+                raise WorkflowError(
+                    "Post deploy script {} provided for conda env {} but unsupported on windows.".format(
+                        post_deploy_script, env_file
+                    )
+                )
+            logger.info(
+                "Running post-deploy script {}...".format(
+                    post_deploy_script.relative_to(os.getcwd())
+                )
+            )
+            conda = Conda(self._container_img)
+            shell.check_output(
+                conda.shellcmd(self.path, "sh {}".format(post_deploy_script)),
+                stderr=subprocess.STDOUT,
+            )
+
     def create(self, dryrun=False):
         """Create the conda enviroment."""
         from snakemake.shell import shell
@@ -374,6 +398,10 @@ def create(self, dryrun=False):
                             "Cleaning up conda package tarballs and package cache."
                         )
                         shell.check_output("conda clean -y --tarballs --packages")
+
+                # Execute post-deplay script if present
+                self.execute_deployment_script(env_file)
+
                 # Touch "done" flag file
                 with open(os.path.join(env_path, "env_setup_done"), "a") as f:
                     pass

tests/test_deploy_script/Snakefile

@@ -0,0 +1,17 @@
+shell.executable("bash")
+
+rule all:
+    input:
+        "test.out"
+
+rule a:
+    output:
+        "test.out"
+    conda:
+        "test-env.yaml"
+    shell:
+        """
+        if [ -f $CONDA_PREFIX/test.txt ] ;then
+            touch {output}
+        fi
+        """

tests/test_deploy_script/test-env.post-deploy.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+touch $CONDA_PREFIX/test.txt

tests/test_deploy_script/test-env.yaml

@@ -0,0 +1,5 @@
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - python <3.10

tests/tests.py

@@ -429,6 +429,11 @@ def test_upstream_conda():
     run(dpath("test_conda"), use_conda=True, conda_frontend="conda")
 
 
+@skip_on_windows
+def test_deploy_script():
+    run(dpath("test_deploy_script"), use_conda=True)
+
+
 def test_conda_custom_prefix():
     run(
         dpath("test_conda_custom_prefix"),