Remove hardcoded HYPHY path. HYPHY should now be a directory under

tool-data (or in our case, a symlink to the real HYPHY dir).

lib/galaxy/tools/util/hyphy_util.py

@@ -11,10 +11,6 @@ def get_filled_temp_filename(contents):
     fh.close()
     return filename
 
-#Hard Coded hyphy path, this will need to be the same across the cluster
-HYPHY_PATH = "/home/universe/linux-i686/HYPHY"
-HYPHY_EXECUTABLE = os.path.join(HYPHY_PATH,"HYPHY")
-
 NJ_tree_shared_ibf = """
 COUNT_GAPS_IN_FREQUENCIES = 0;
 methodIndex				  = 1;
@@ -1026,4 +1022,4 @@ _genomeScreenOptions ["3"] = "%s";
 	
 ExecuteAFile ("%s", _genomeScreenOptions);		
 """ % (input_filename, output_filename1, output_filename2, distance_metric, NJ_tree_filename)
-    return get_filled_temp_filename(contents)
+    return get_filled_temp_filename(contents)

tools/hyphy/hyphy_branch_lengths_wrapper.py

@@ -4,9 +4,10 @@ import os, sys
 from galaxy import eggs
 from galaxy.tools.util import hyphy_util
 
-#Retrieve hard coded hyphy path, this will need to be the same across the cluster
-HYPHY_PATH = hyphy_util.HYPHY_PATH
-HYPHY_EXECUTABLE = hyphy_util.HYPHY_EXECUTABLE
+#Retrieve hyphy path, this will need to be the same across the cluster
+tool_data = sys.argv.pop()
+HYPHY_PATH = os.path.join( tool_data, "HYPHY" )
+HYPHY_EXECUTABLE = os.path.join( HYPHY_PATH, "HYPHY" )
 
 #Read command line arguments
 input_filename = os.path.abspath(sys.argv[1].strip())

tools/hyphy/hyphy_branch_lengths_wrapper.xml

@@ -3,7 +3,7 @@
 	
 	<description>Estimation</description>
 	
-	<command interpreter="python">hyphy_branch_lengths_wrapper.py $input1 $out_file1 "$tree" "$model" "$base_freq" "Global"</command>
+	<command interpreter="python">hyphy_branch_lengths_wrapper.py $input1 $out_file1 "$tree" "$model" "$base_freq" "Global" ${GALAXY_DATA_INDEX_DIR}</command>
 	
     <inputs>
         <page>

tools/hyphy/hyphy_dnds_wrapper.py

@@ -4,9 +4,10 @@ import os, sys
 from galaxy import eggs
 from galaxy.tools.util import hyphy_util
 
-#Retrieve hard coded hyphy path, this will need to be the same across the cluster
-HYPHY_PATH = hyphy_util.HYPHY_PATH
-HYPHY_EXECUTABLE = hyphy_util.HYPHY_EXECUTABLE
+#Retrieve hyphy path, this will need to be the same across the cluster
+tool_data = sys.argv.pop()
+HYPHY_PATH = os.path.join( tool_data, "HYPHY" )
+HYPHY_EXECUTABLE = os.path.join( HYPHY_PATH, "HYPHY" )
 
 #Read command line arguments
 input_filename = os.path.abspath(sys.argv[1].strip())

tools/hyphy/hyphy_dnds_wrapper.xml

@@ -3,7 +3,7 @@
 	
 	<description>Estimation</description>
 	
-	<command interpreter="python">hyphy_dnds_wrapper.py $input1 $out_file1 "$tree" "$model" $analysis</command>
+	<command interpreter="python">hyphy_dnds_wrapper.py $input1 $out_file1 "$tree" "$model" $analysis ${GALAXY_DATA_INDEX_DIR}</command>
 	
     <inputs>
         <page>

tools/hyphy/hyphy_nj_tree_wrapper.py

@@ -4,9 +4,10 @@ import os, sys
 from galaxy import eggs
 from galaxy.tools.util import hyphy_util
 
-#Retrieve hard coded hyphy path, this will need to be the same across the cluster
-HYPHY_PATH = hyphy_util.HYPHY_PATH
-HYPHY_EXECUTABLE = hyphy_util.HYPHY_EXECUTABLE
+#Retrieve hyphy path, this will need to be the same across the cluster
+tool_data = sys.argv.pop()
+HYPHY_PATH = os.path.join( tool_data, "HYPHY" )
+HYPHY_EXECUTABLE = os.path.join( HYPHY_PATH, "HYPHY" )
 
 #Read command line arguments
 input_filename = os.path.abspath(sys.argv[1].strip())

tools/hyphy/hyphy_nj_tree_wrapper.xml

@@ -3,7 +3,7 @@
     
     <description>Builder</description>
     
-    <command interpreter="python">hyphy_nj_tree_wrapper.py $input1 $out_file1 $out_file2 $distance_metric</command>
+    <command interpreter="python">hyphy_nj_tree_wrapper.py $input1 $out_file1 $out_file2 $distance_metric ${GALAXY_DATA_INDEX_DIR}</command>
     
     <inputs>
         <page>