Merge pull request #378 from andrewjpage/version_fix

fix mafft and kraken version extraction

Author: andrewjpage

dist.ini

@@ -3,7 +3,7 @@ author  = Andrew J. Page <ap13@sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
 copyright_year   = 2013
-version = 3.11.1
+version = 3.11.2
 main_module = lib/Bio/Roary.pm
 
 [MetaResources]

lib/Bio/Roary/External/CheckTools.pm

@@ -57,17 +57,17 @@ my %tools = (
     },
     'mafft' => {
         GETVER => "mafft --version < /dev/null 2>&1",
-        REGEXP => qr/(\d+\.\d+) /,
+        REGEXP => qr/(\d+\.\d+)/,
         NEEDED => 1,
     },
     'kraken' => {
-        GETVER => "kraken --version | head -n 1",
+        GETVER => "kraken -v | head -n 1",
         REGEXP => qr/(\d+\.\d+\.\d+.*)/,
         NEEDED => 0,
     },
     'kraken-report' => {
         GETVER => "kraken-report --version | head -n 1",
-        REGEXP => qr/(\d+\.\d+\.\d+.*)/,
+        REGEXP => qr/Kraken version (\d+\.\d+\.*\d*.*)/,
         NEEDED => 0,
     },
 	'Rscript'  => {