Minor bug fixes to setting up reference data.

checkm/VERSION

@@ -1,3 +1,7 @@
+1.1.2
+- removed erroneous error message when setting root to CheckM reference data
+- fixed infinit loop issue when trying to install CheckM reference data to directory without write permission
+
 1.1.1
 - fixes legacy Python 2 syntax issues (thanks to Sebastian Jaenicke!)
 

checkm/checkmData.py

@@ -179,6 +179,7 @@ def confirmPath(self, path=None):
                     print ("Path [%s] exists and you have permission to write to this folder." % path)
                 else:
                     print ("Path [%s] exists but you do not have permission to write to this folder." % path)
+                    sys.exit(-1)
             else:
                 # path does not exist, try to make it
                 print ("Path [%s] does not exist so I will attempt to create it" % path)
@@ -187,7 +188,7 @@ def confirmPath(self, path=None):
                     print ("Path [%s] has been created and you have permission to write to this folder." % path)
                     path_set = True
                 except Exception:
-                    print ("Unable to make the folder, Error was: %s" % sys.exc_info()[0])
+                    print ("Unable to make the folder; error was: %s" % sys.exc_info()[0])
                 minimal = True
 
         # (re)make the manifest file

checkm/main.py

@@ -76,6 +76,7 @@ def updateCheckM_DB(self, options):
         action = options.action
         if action and action[0] == 'setRoot' and len(action) > 1:
             DBM = DBManager(set_path=action[1])
+        else:
             self.logger.error('Path to the CheckM reference data must be specified.')
 
     def binFiles(self, binFolder, binExtension):