Add possibility to give a logger to utils.run_cmd().

By default, it uses the default logger. But, when called from a different process, it should use the given logger, which will give information to a queue

genomeAPCAT/utils.py

@@ -182,7 +182,8 @@ def run_cmd(cmd, error, eof=False, **kwargs):
     Run the given command line. If the return code is not 0, print error message.
     if eof (exit on fail) is True, exit program if error code is not 0.
     """
-    logger = logging.getLogger("utils.run_cmd")
+    if not "logger" in kwargs:
+        logger = logging.getLogger("utils.run_cmd")
     if not "stdout" in kwargs:
         kwargs["stdout"] = None
     if not "stderr" in kwargs: