# HG changeset patch
# User trinity_ctat
# Date 1505504901 14400
# Node ID 2a3972086548d0bbcddc4b72634b7bc230bd9cb2
# Parent  1e638acde0cf8787a479c1c05450b963fee8c549
Test concatenate changes

diff -r 1e638acde0cf -r 2a3972086548 bash_command_executer.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bash_command_executer.py	Fri Sep 15 15:48:21 2017 -0400
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+
+import sys, subprocess, os
+
+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" )
+
+    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__()
diff -r 1e638acde0cf -r 2a3972086548 concatenate.xml
--- a/concatenate.xml	Fri Sep 15 15:28:26 2017 -0400
+++ b/concatenate.xml	Fri Sep 15 15:48:21 2017 -0400
@@ -1,10 +1,11 @@
-<tool id="catbash" name="Concatenate datasets">
+<tool id="catbash" name="Concatenate datasets" version="2.0">
     <description> concatenate datasets from tail to head</description>
-    <!--    bash_command_executer.py cat
-    -->
+    <requirements>
+        <requirement type="package">python</requirement>
+    </requirements>
     <command>
       <![CDATA[
-        cat
+        bash_command_executer.py cat
         $input1
         #for $q in $queries
             ${q.input2}