# HG changeset patch
# User trinity_ctat
# Date 1506452073 14400
# Node ID 28f6d3b8e931c4b7e4c7d6c24d394a7c8f6eaa4c
# Parent  78d12a7254437976383385592f4c6a10a5c180d5
Adjusting requirements.

diff -r 78d12a725443 -r 28f6d3b8e931 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Tue Sep 26 14:31:27 2017 -0400
+++ b/align_and_estimate_abundance.xml	Tue Sep 26 14:54:33 2017 -0400
@@ -5,10 +5,9 @@
     <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>
+        <requirement type="package">bowtie2</requirement>
+        <requirement type="package">samtools</requirement>
+        <requirement type="package">rsem</requirement>
     </requirements>
 
     <command interpreter="python">
diff -r 78d12a725443 -r 28f6d3b8e931 trinityToolWrapper.py
--- a/trinityToolWrapper.py	Tue Sep 26 14:31:27 2017 -0400
+++ b/trinityToolWrapper.py	Tue Sep 26 14:54:33 2017 -0400
@@ -24,8 +24,9 @@
     try:
         pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
     except:
+        msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.".format(sys.argv[0])
+        sys.stderr.write(msg)
         t, v, tb = sys.exc_info()
-        sys.stderr.write("You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.".format(sys.argv[0]))
         raise t, v, tb
     else:
         TrinityPath, err_info = pipe1.communicate()