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/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 &gt; $logFile 

works like a charme - problem solved! Thanks Peter!!!


-----Urspr√ľngliche 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 "&amp;&gt;" 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":
> &amp;>
> &amp;&gt;
> &#38;&#62;
> 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 &amp;&gt; $logFile</command>


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