# HG changeset patch
# User trinity_ctat
# Date 1506450687 14400
# Node ID 78d12a7254437976383385592f4c6a10a5c180d5
# Parent  12bc09b4a26d8cc30eb1320f500ec12c9615f2ca
Adding additional requirements for align_and_estimate_abundance.

diff -r 12bc09b4a26d -r 78d12a725443 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Tue Sep 26 13:58:08 2017 -0400
+++ b/align_and_estimate_abundance.xml	Tue Sep 26 14:31:27 2017 -0400
@@ -5,6 +5,10 @@
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
         <requirement type="package" version="2.4.0">trinity</requirement>
+        <requirement type="package" version="2">bowtie</requirement>
+        <requirement type="package" >samtools</requirement>
+        <!-- <requirement type="package" >express</requirement> -->
+        <requirement type="package" >rsem</requirement>
     </requirements>
 
     <command interpreter="python">
diff -r 12bc09b4a26d -r 78d12a725443 trinityToolWrapper.py
--- a/trinityToolWrapper.py	Tue Sep 26 13:58:08 2017 -0400
+++ b/trinityToolWrapper.py	Tue Sep 26 14:31:27 2017 -0400
@@ -45,7 +45,9 @@
         # Take off the last part of the path (which is the Trinity command)
         TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
 else:
-    print "Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH."
+    sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.")
+    sys.exit()
+
 
 # get bindir
 bindir = sys.argv[0]