--- a/mugsy.py	Mon Sep 09 05:40:19 2013 -0400
+++ b/mugsy.py	Fri Oct 25 06:39:33 2013 -0400
@@ -13,7 +13,6 @@
 import tempfile
 
 def __main__():
-    """ main function """
     parser = optparse.OptionParser()
     parser.add_option('-r', dest='reference', help='reference FASTA file')
     parser.add_option('-c', dest='contigs', help='contigs FASTA file')
@@ -24,13 +23,13 @@
     (options, args) = parser.parse_args()
     if len(args) > 0:
         parser.error('Wrong number of arguments')
-    
+
     logfile = options.logfile
     wd = tempfile.mkdtemp()
     try:
         command = "mugsy --directory %s --prefix %s --log %s %s %s" % (wd, options.prefix, options.mugsylog, options.reference, options.contigs)
         print 'Mugsy command to be executed:\n ' + command
-        
+
         log = open(logfile, 'w') if logfile else sys.stdout
         try:
             subprocess.check_call(command, stderr=log, shell=True) # need to redirect stderr because mugsy writes its logging info there
@@ -38,7 +37,7 @@
             if log != sys.stdout:
                 log.close()
         print 'Mugsy executed!'
-        
+
         shutil.move(os.path.join(wd, options.prefix + '.maf'), options.maf)
     finally:
         shutil.rmtree(wd)

--- a/mugsy.xml	Mon Sep 09 05:40:19 2013 -0400
+++ b/mugsy.xml	Fri Oct 25 06:39:33 2013 -0400
@@ -1,6 +1,7 @@
 <tool id="mugsy" name="Mugsy" version="1.0.1">
   <description>multiple whole genome aligner</description>
   <requirements>
+    <requirement type="package" version="1.53.0">boost</requirement>
     <requirement type="package" version="1.2.3.1">mugsy</requirement>
   </requirements>
   <command interpreter="python">