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!


-----Urspr√ľngliche Nachricht-----
Von: Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Gesendet: Montag, 24. Oktober 2011 12:06
An: Appelt, Uwe
Cc: galaxy-user@lists.bx.psu.edu; 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 &amp;&gt; $logFile</command>
> <command interpreter="sh">$hisapWrapperScript &amp;&gt; $logFile</command>
> <command>bash $hisapWrapperScript &amp;&gt; $logFile</command>
> <command>sh $hisapWrapperScript &amp;&gt; $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 &amp;&gt; $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:

> Aaaaaah, but the different redirection syntax works. So to conclude:
> <command interpreter="bash">$hisapWrapperScript &gt; $logFile 
> 2&gt;&amp;1</command>
> works like a charme - problem solved! Thanks Peter!!!
> Cheers,
> Uwe

Glad you got there in the end :)


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.

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