Merge pull request #1428 from bernt-matthias/topic/docker-extra-args

Add option to pass extra arguments to `docker run`
galaxyproject · Feb 8, 2024 · e69487c · e69487c
2 parents 023c758 + 08eaf62
commit e69487c
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diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
@@ -130,6 +130,7 @@
             <param id="docker_sudo_cmd">${docker_sudo_cmd}</param>
             <param id="docker_cmd">${docker_cmd}</param>
             <param id="docker_volumes">${docker_volumes}</param>
+            <param id="docker_run_extra_arguments"><![CDATA[${docker_run_extra_arguments}]]></param>
             ${docker_host_param}
         </destination>
         <destination id="upload_dest" runner="planemo_runner">
@@ -1363,6 +1364,7 @@ def _handle_job_config_file(
                 "docker_cmd": str(kwds.get("docker_cmd", docker_util.DEFAULT_DOCKER_COMMAND)),
                 "docker_host_param": docker_host_param,
                 "docker_volumes": docker_volumes_str,
+                "docker_run_extra_arguments": kwds.get("docker_run_extra_arguments", ""),
             }
         )
         write_file(job_config_file, conf_contents)

diff --git a/planemo/options.py b/planemo/options.py
@@ -956,12 +956,22 @@ def docker_host_option():
     )
 
 
+def docker_run_extra_arguments_option():
+    return planemo_option(
+        "--docker_run_extra_arguments",
+        help="Extra arguments to pass to docker run.",
+        use_global_config=True,
+        default="",
+    )
+
+
 def docker_config_options():
     return _compose(
         docker_cmd_option(),
         docker_sudo_option(),
         docker_host_option(),
         docker_sudo_cmd_option(),
+        docker_run_extra_arguments_option(),
     )