--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wrapper.sh	Sat Oct 06 21:50:39 2012 +0200
@@ -0,0 +1,33 @@
+#!/bin/sh
+
+# STDERR wrapper - discards STDERR if command execution was OK.
+
+#
+# This script executes a given command line,
+# while saving the STDERR in a temporary file.
+#
+# When the command is completed, it checks to see if the exit code was zero.
+# if so - the command is assumed to have succeeded - the STDERR file is discarded.
+# if not - the command is assumed to have failed, and the STDERR file is dumped to the real STDERR
+#
+#
+# Use this wrapper for tools which insist on writting stuff to STDERR
+# even if they succeeded -
+# which throws galaxy off balance.
+#
+#
+# Copyright 2009 (C) by Assaf Gordon
+# This file is distributed under the BSD license.
+
+TMPFILE=$(mktemp) || exit 1
+
+"$@" 2> $TMPFILE
+
+EXITCODE=$?
+# Exitcode != 0 ?
+if [ "$EXITCODE" -ne "0" ]; then
+       cat $TMPFILE >&2
+fi
+rm $TMPFILE
+
+exit $EXITCODE