Split the command if its a single, non-json-parseable string.

1 files changed, 6 insertions, 1 deletions

diff --git a/gn3/commands.py b/gn3/commands.py
index 38153bf..51b70c3 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -3,6 +3,7 @@ commands"""
 import os
 import sys
 import json
+import shlex
 import pickle
 import logging
 import tempfile
@@ -156,7 +157,11 @@ def run_sample_corr_cmd(method, this_trait_data, target_dataset_data):
 
 def run_cmd(cmd: str, success_codes: Tuple = (0,), env: Optional[str] = None) -> Dict:
     """Run CMD and return the CMD's status code and output as a dict"""
-    parsed_cmd = json.loads(__pk__("Attempting to parse command", cmd))
+    try:
+        parsed_cmd = json.loads(__pk__("Attempting to parse command", cmd))
+    except json.decoder.JSONDecodeError as jderr:
+        parsed_cmd = shlex.split(cmd)
+
     parsed_env = (json.loads(env) if env is not None else None)
 
     results = subprocess.run(