Fixes to get functional tests working.

tools/hyphy/hyphy_branch_lengths_wrapper.xml

@@ -1,4 +1,4 @@
-<?xml version="1.1.0"?>
+<?xml version="1.2.0"?>
 <tool name="Branch Lengths" id="hyphy_branch_lengths_wrapper1">
 	
 	<description>Estimation</description>

tools/regVariation/getIndels.py

@@ -10,8 +10,10 @@ from __future__ import division
 from galaxy import eggs
 import pkg_resources 
 pkg_resources.require( "bx-python" )
-pkg_resources.require("numpy")
-
+try:
+    pkg_resources.require("numpy")
+except:
+    pass
 import psyco_full
 import sys
 from bx.cookbook import doc_optparse

tools/regVariation/quality_filter.py

@@ -12,7 +12,10 @@ from galaxy import eggs
 import pkg_resources 
 pkg_resources.require( "bx-python" )
 pkg_resources.require( "lrucache" )
-pkg_resources.require("numpy")
+try:
+    pkg_resources.require("numpy")
+except:
+    pass
 
 import psyco_full
 import sys