Well, no, I didn't try to specify neither an "interpreter=" nor the actual shell-binary as part of the command-tag itself, because I'm assembling the shell-script dynamically within a configfile-tag. Thus, I do not see any chance to apply an "executable"-flag to that script that is infact filed to disk by the galaxy-job-scheduler somewhen in the future. So it's not that you were too vague, I just that didn't know how to embed your idea into xml/shell-code.
But as you already mentioned, I made it with the slightly more verbose notation and that's great. Thanks again, Peter! Cheers, Uwe -----Ursprüngliche Nachricht----- Von: Peter Cock [mailto:p.j.a.c...@googlemail.com] Gesendet: Montag, 24. Oktober 2011 12:06 An: Appelt, Uwe Cc: firstname.lastname@example.org; galaxy-...@lists.bx.psu.edu Betreff: Re: [galaxy-user] tool.xml "&>" console redirection within command-tag Hi Uwe, On Mon, Oct 24, 2011 at 10:47 AM, Appelt, Uwe <uwe.app...@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. ___________________________________________________________ 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/