Minor bug fixes to 'test' and 'data setRoot' commands.

checkm/DATA_CONFIG

@@ -1 +1 @@
-{"dataRoot": "/srv/db/checkm_data/0.9.7", "remoteManifestURL": "https://data.ace.uq.edu.au/public/CheckM_databases/", "manifestType": "CheckM", "localManifestName": ".dmanifest", "remoteManifestName": ".dmanifest"}
+{"dataRoot": "/srv/db/checkm_data/1.0.0", "remoteManifestURL": "https://data.ace.uq.edu.au/public/CheckM_databases/", "manifestType": "CheckM", "remoteManifestName": ".dmanifest", "localManifestName": ".dmanifest"}

checkm/VERSION

@@ -1 +1 @@
-1.0.5
+1.0.6

checkm/checkmData.py

@@ -174,7 +174,7 @@ def setRoot(self, path=None):
             return None
 
         # validate the supplied path or prompt for a new one
-        path = self.confirmPath(path=path)
+	path = self.confirmPath(path=path)
         if path is None:
             # The user is not interested
             return None
@@ -192,11 +192,12 @@ def confirmPath(self, path=None):
         path_set = False
         minimal = False
         while not path_set:
-            if(minimal):
-                path = raw_input("Please specify a location or type 'abort' to stop trying: \n")
-            else:
-                path = raw_input("Where should CheckM store it's data?\n" \
-                                 "Please specify a location or type 'abort' to stop trying: \n")
+            if not path:
+	    	if(minimal):
+                    path = raw_input("Please specify a location or type 'abort' to stop trying: \n")
+            	else:
+                    path = raw_input("Where should CheckM store it's data?\n" \
+                    	             "Please specify a location or type 'abort' to stop trying: \n")
 
             if path.upper() == "ABORT":
                 # user has given up

checkm/hmmer.py

@@ -99,6 +99,10 @@ def fetch(self, db, key, fetchFileName, bKeyFile=False):
 
         os.system('hmmfetch ' + keyFileOpt + ' %s %s > %s' % (db, key, fetchFileName))
 
+    def press(self, hmmModelFile):
+        """Press a HMM file."""
+        os.system('hmmpress %s > /dev/null' % hmmModelFile)
+
     def index(self, hmmModelFile):
         """Index a HMM file."""
         if self.mode != 'fetch':

checkm/test/test_ecoli.py

@@ -49,6 +49,7 @@ def run(self, parser, outputDir):
 
         options = Options()
         options.threads = 1
+	options.pplacer_threads = 1
         options.extension = 'fna'
         options.bQuiet = True
         options.out_folder = os.path.join(outputDir, 'results')