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 &> $logFile</command> I get a according debug-line in the galaxy.log, reporting something like: galaxy.jobs.runners.local DEBUG 2011-10-24 11:26:55,360 executing: bash /home/extuser/www/galaxy/galaxy_working/database/job_working_directory/2222/tmpZmFMfg &> /home/extuser/www/galaxy/galaxy_working/database/files/005/dataset_5410.dat So the "&>" definitely makes it through XML, Cheetah, etc. -parsers and finally to the cmd-line. However, neither BASH nor SH produce a log-file as intended. For some strange reason (Peter, you're right again) all log-lines appear in the green box. And even more, the green box turns of course red as soon as something is written to stderr. Aaaaaah, but the different redirection syntax works. So to conclude: <command interpreter="bash">$hisapWrapperScript > $logFile 2>&1</command> works like a charme - problem solved! Thanks Peter!!! Cheers, Uwe -----Ursprüngliche Nachricht----- Von: Peter Cock [mailto:p.j.a.c...@googlemail.com] Gesendet: Montag, 24. Oktober 2011 11:07 An: Appelt, Uwe Cc: galaxy-user@lists.bx.psu.edu Betreff: Re: [galaxy-user] tool.xml "&>" console redirection within command-tag On Mon, Oct 24, 2011 at 9:42 AM, Appelt, Uwe <uwe.app...@nct-heidelberg.de> wrote: > Hi Peter, > > thanks a lot for your quick reply. However "&>" doesn't > seem to work as well. Also, I do have to admit that two different > "doesn't work" exist. > > Notations that are not accepted during parsing of toolxy.xml: > &> > \&> > \\&> > > Notations that are accepted, but don't produce any content written > to "$logFile": > &> > &> > &> > > Any other suggestions? > > Cheers, > Uwe Curious. Well, at least you seem to have valid XML now (double check this with an XML validator). Does Galaxy capture anything in the "info" box (stdout)? There are some variants like 2>&1 for redirecting stderr to stdout, try combining that with > logfile. My *guess* however is the interpreter="bash" may be to blame, try this after ensuring the script is executable and on the path or fully specified: <command>$myScript &> $logFile</command> Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
