Hi Uwe, On Mon, Oct 24, 2011 at 10:47 AM, Appelt, Uwe <uwe.appelt@nct-heidelberg.de> wrote:
Hi again,
yes, you're right. The problem source is something else. As soon as I specify one of the following
<command interpreter="bash">$hisapWrapperScript &> $logFile</command> <command interpreter="sh">$hisapWrapperScript &> $logFile</command> <command>bash $hisapWrapperScript &> $logFile</command> <command>sh $hisapWrapperScript &> $logFile</command>
I get a according debug-line in the galaxy.log, reporting something like:
galaxy.jobs.runners.local DEBUG 2011-10-24 11:26:55,360 executing: bash /home/extuser/www/galaxy/galaxy_working/database/job_working_directory/2222/tmpZmFMfg &> /home/extuser/www/galaxy/galaxy_working/database/files/005/dataset_5410.dat
So the "&>" definitely makes it through XML, Cheetah, etc. -parsers and finally to the cmd-line. However, neither BASH nor SH produce a log-file as intended.
You didn't try the precise combination I meant, <command>$hisapWrapperScript &> $logFile</command> where $hisapWrapperScript is marked as executable and has a Unix hashbang line saying which shell to use, e.g. #!/usr/bin/bash Apologies if I was too vague.
For some strange reason (Peter, you're right again) all log-lines appear in the green box.
To be expected, Galaxy captures any stdout (assuming nothing else captured it first) and puts it in the info field.
And even more, the green box turns of course red as soon as something is written to stderr.
Yes, it is a long standing Galaxy bug that any stderr out is treated as an error condition, rather than looking at the return code: https://bitbucket.org/galaxy/galaxy-central/issue/325/
Aaaaaah, but the different redirection syntax works. So to conclude:
<command interpreter="bash">$hisapWrapperScript > $logFile 2>&1</command>
works like a charme - problem solved! Thanks Peter!!!
Cheers, Uwe
Glad you got there in the end :) Peter By the way - this whole discussion would have been better suited to the galaxy-dev list (CC'd) since it is about developing tools for Galaxy rather than Galaxy end users.