Branden, The current Galaxy job runner does not respect the tool unix exit flag unfortunately and will assume an error if the tool writes anything to stderr - there's a ticket on this but no progress at http://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-t... - writing to stdout should (AFAIK) not cause the job to error out? Escaping redirection on the command line param is a pain, but you could (eg) use something based on the shell code in tools/bigbedwig/discard_stderr_wrapper.sh written by Assaf Gordon - see below? [rerla@beast galaxy]$ cat tools/bigbedwig/discard_stderr_wrapper.sh #!/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 On Fri, Sep 3, 2010 at 12:53 PM, Branden Timm <btimm(a)wisc.edu&gt; wrote: > Hello, > I'm writing some wrappers for Galaxy and am finding it difficult to debug > proper redirection of stderr and stdout in my wrapper subprocesses. When > Galaxy detects an error running a tool, it highlights the output files in > red and gives you the "bug" icon so that you can view stderr and stdout. > However, when Galaxy interprets the tool as having run successfully, I'm > unable to find a way to view what was in stdout. > > Long story short, Galaxy is interpreting my tool to have run successfully > even when it hasn't. I'm redirecting stderr to sdtout on my <command> line > in the tool conf file so that Galaxy only relies on return codes to detect > an error in the tool, not stderr. > > Is there a way to view stdout when a tool has run "successfully"? > > Cheers > > -- > Branden Timm > Great Lakes Bioenergy Research Center > btimm(a)glbrc.wisc.edu > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev > >