docker cmd

snakemake_executor_plugin_aws_batch/__init__.py

@@ -4,7 +4,6 @@
 __license__ = "MIT"
 
 from dataclasses import dataclass, field
-import shlex
 from pprint import pformat
 from typing import List, AsyncGenerator, Optional
 from snakemake_executor_plugin_aws_batch.batch_client import BatchClient
@@ -132,8 +131,7 @@ def run_job(self, job: JobExecutorInterface):
         # If required, make sure to pass the job's id to the job_info object, as keyword
         # argument 'external_job_id'.
 
-        remote_command = f"/bin/bash -c {shlex.quote(self.format_job_exec(job))}"
-        self.logger.debug(f"Remote command: {remote_command}")
+        remote_command = f"/bin/bash -c {self.format_job_exec(job)}"
 
         try:
             job_definition = BatchJobBuilder(
@@ -212,10 +210,12 @@ def _get_job_status(self, job: SubmittedJobInfo) -> tuple[int, Optional[str]]:
         exit_code = None
         log_stream_name = None
         job_desc = self._describer.describe(self.batch_client, job.external_jobid, 1)
+        self.logger.debug(f"JOB DESCRIPTION: {job_desc}")
         job_status = job_desc["status"]
 
         # set log stream name if not none
         log_details = {"status": job_status, "jobId": job.external_jobid}
+        self.logger.debug(f"LOG DETAILS: {log_details}")
 
         if "container" in job_desc and "logStreamName" in job_desc["container"]:
             log_stream_name = job_desc["container"]["logStreamName"]

snakemake_executor_plugin_aws_batch/batch_job_builder.py

@@ -1,4 +1,6 @@
 import uuid
+import shlex
+from typing import List
 from snakemake.exceptions import WorkflowError
 from snakemake_interface_executor_plugins.jobs import (
     JobExecutorInterface,
@@ -43,6 +45,12 @@ def __init__(
         self.batch_client = batch_client
         self.created_job_defs = []
 
+    def _make_container_command(remote_command: str) -> List[str]:
+        """
+        Return docker CMD form of the command
+        """
+        return [shlex.quote(part) for part in shlex.split(str)]
+
     def build_job_definition(self):
         job_uuid = str(uuid.uuid4())
         job_name = f"snakejob-{self.job.name}-{job_uuid}"
@@ -55,7 +63,8 @@ def build_job_definition(self):
 
         container_properties = {
             "image": self.container_image,
-            "command": [self.job_command],
+            # command requires a list of strings ( docker CMD format )
+            "command": self._make_container_command(self.job_command),
             "jobRoleArn": self.settings.job_role,
             "privileged": True,
             "resourceRequirements": [