Fix various things about the hgv_ldtools tool

Unfortnately this doens't produce the test-data output on python 3 and
so I added a requiremtn on python 2. (I think the result is probably
correct but not deterministic).

tools/phenotype_association/ldtools.xml

@@ -1,8 +1,10 @@
 <tool id="hgv_ldtools" name="LD" version="1.0.0">
   <description>linkage disequilibrium and tag SNPs</description>
-
-  <command interpreter="bash">
-    ldtools_wrapper.sh rsquare=$rsquare freq=$freq input=$input output=$output
+  <requirements>
+    <requirement type="package" version="2.7">python</requirement>
+  </requirements>
+  <command detect_errors="exit_code">
+'$__tool_directory__/ldtools_wrapper.sh' rsquare=$rsquare freq=$freq input='$input' output='$output'
   </command>
 
   <inputs>

tools/phenotype_association/ldtools_wrapper.sh

@@ -5,7 +5,7 @@
 
 set -e
 
-export PATH=$PATH:$(dirname $0)
+SCRIPT_DIR=$(dirname $0)
 
 ## pagetag options
 input=
@@ -46,19 +46,16 @@ do
 done
 
 ## run pagetag
-pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt &> /dev/null
+python $SCRIPT_DIR/pagetag.py --rsquare $rsquare --freq $freq "$input" snps.txt neighborhood.txt
 if [ $? -ne 0 ]; then
-	echo "failed: pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt"
+	echo "failed: pagetag.py --rsquare $rsquare --freq $freq \"$input\" snps.txt neighborhood.txt"
 	exit 1
 fi
 
 ## run sentag
-senatag.py neighborhood.txt snps.txt > $output 2> /dev/null
+python $SCRIPT_DIR/senatag.py neighborhood.txt snps.txt > "$output"
 if [ $? -ne 0 ]; then
 	echo "failed: senatag.py neighborhood.txt snps.txt"
 	exit 1
 fi
 
-## cleanup
-rm -f snps.txt neighborhood.txt
-

tools/phenotype_association/senatag.py

@@ -25,6 +25,7 @@ from __future__ import print_function
 
 import heapq
 import os
+from functools import total_ordering
 from getopt import getopt, GetoptError
 from sys import argv, exit, stderr
 
@@ -35,6 +36,7 @@ __email__ = "ratan@bx.psu.edu"
 debug_flag = False
 
 
+@total_ordering
 class node:
     def __init__(self, name):
         self.name = name
@@ -50,8 +52,14 @@ class node:
                 num += 1
         return num
 
-    def __cmp__(self, other):
-        return other.num_not_visited() - self.num_not_visited()
+    def __eq__(self, other):
+        return self.num_not_visited() == other.num_not_visited()
+
+    def __ne__(self, other):
+        return not (self == other)
+
+    def __lt__(self, other):
+        return other.num_not_visited() < self.num_not_visited()
 
     def __str__(self):
         return self.name
@@ -165,7 +173,7 @@ def main(ldfile, snpsfile, required, excluded):
         neighbors[t.name] = list(set(ns))
 
     # find the tag SNPs for this graph
-    data = g.nodes.values()[:]
+    data = list(g.nodes.values())[:]
     heapq.heapify(data)
 
     while data: