# HG changeset patch
# User gkumar09
# Date 1443492145 14400
# Node ID ecf8be6538f84485d498cc22cb44714e33d779dc
# Parent  e281bf1764217026f1cfaa71afed256a1f8381df
Deleted selected files

diff -r e281bf176421 -r ecf8be6538f8 Final/trinityToolWrapper.py
--- a/Final/trinityToolWrapper.py	Mon Sep 28 21:55:19 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-#!/usr/bin/env python
-
-
-# borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools.
-
-"""
-Wrapper that execute a program and its arguments but reports standard error
-messages only if the program exit status was not 0
-Example: ./stderr_wrapper.py myprog arg1 -f arg2
-"""
-
-import sys, subprocess, os
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-TRINITY_BASE_DIR = ""
-if os.environ.has_key('TRINITY_HOME'):
-    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
-else:
-    sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
-    sys.exit()
-
-
-
-# get bindir
-bindir = sys.argv[0]
-bindir = bindir.split("/")
-if len(bindir) > 1:
-    bindir.pop()
-    bindir = "/".join(bindir)
-else:
-    bindir = "."
-
-
-## add locations of tools to path setting.
-TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt";
-for line in open(TOOL_PATHS_FILE):
-    line = line.rstrip()
-    os.environ['PATH'] += ":" + line
-
-
-def stop_err( msg ):
-    sys.stderr.write( "%s\n" % msg )
-    sys.exit()
-
-def __main__():
-    # Get command-line arguments
-    args = sys.argv
-    # Remove name of calling program, i.e. ./stderr_wrapper.py
-    args.pop(0)
-    # If there are no arguments left, we're done
-    if len(args) == 0:
-        return
-
-    # If one needs to silence stdout 
-    #args.append( ">" )
-    #args.append( "/dev/null" )
-
-    args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]);
-
-    cmdline = " ".join(args)
-
-    
-
-    try:
-        # Run program
-        err_capture = open("stderr.txt", 'w')
-        proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout )
-        returncode = proc.wait()
-        err_capture.close()
-
-        
-        if returncode != 0:
-            raise Exception
-
-    except Exception:
-        # Running Grinder failed: write error message to stderr
-        err_text = open("stderr.txt").readlines()
-        stop_err( "ERROR:\n" + "\n".join(err_text))
-
-
-if __name__ == "__main__": __main__()