annotate wrapper.sh @ 19:cc270db37d33 draft

Directories re-arranged

#!/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