Mercurial > repos > lparsons > cutadapt
view discard_stderr_wrapper.sh @ 4:0a872e59164c
Added discard_stderr_wrapper.sh script to catch report and redirect to stdout
author | Lance Parsons <lparsons@princeton.edu> |
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date | Wed, 25 May 2011 19:33:40 -0400 |
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#!/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. # # Modified by Lance Parsons (2011) # Echo STDERR to STDOUT if return code was 0 TMPFILE=$(mktemp -t tmp.XXXXXXXXXX) || exit 1 #CWD=`pwd` #DIRECTORY=$(cd `dirname $0` && pwd) #cd $DIRECTORY "$@" 2> $TMPFILE EXITCODE=$? # Exitcode != 0 ? if [ "$EXITCODE" -ne "0" ]; then cat $TMPFILE >&2 else # echo "Testing STDOUT" cat $TMPFILE >&1 fi rm $TMPFILE cd $CWD exit $EXITCODE