Update for python 3.6

.gitignore

@@ -7,4 +7,5 @@ ENV/
 env.bak/
 venv.bak/
 .idea
-config_phaeoexplorer*
+config_phaeoexplorer*
\ No newline at end of file
+*.pyc

utilities.py

@@ -94,7 +94,7 @@ def check_galaxy_state(genus_lowercase, species, script_dir):
 
     # Run supervisorctl status in the galaxy container via serexec
     galaxy_logs = subprocess.run(["%s/serexec" % script_dir, "{0}_{1}_galaxy".format(genus_lowercase, species),
-                                  "supervisorctl", "status", "galaxy:"], capture_output=True)
+                                  "supervisorctl", "status", "galaxy:"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     if "galaxy:galaxy_web                RUNNING" in str(galaxy_logs.stdout) \
             and "galaxy:handler0                  RUNNING" in str(galaxy_logs.stdout) \
             and "galaxy:handler1                  RUNNING" in str(galaxy_logs.stdout):