Adding galaxy-dist/tools/${category} to PATH before calling sh run.sh does the 
trick. This is not ideal but works for now...

Thanks,
Manuel
________________________________________
From: Björn Grüning [bjoern.gruen...@pharmazie.uni-freiburg.de]
Sent: Thursday, April 11, 2013 12:19 AM
To: Holtgrewe, Manuel
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] "Local install" of Galaxy Tool

Hi,

> I have:
>
> galaxy-dist/tools/${category}/BINARY
> galaxy-dist/tools/${category}/BINARY.xml

Try to put the binary in your PATH.

> Where BINARY.xml contains the <tool ...><command>BINARY... XML code.
>
> Is there a good way to see what Galaxy is exactly executing for the tool?

In your webX.log. It is depending on your configuration, but in your log
file the executed command is logged.

> I could not find a description on how to do that anywhere on the internet 
> (*sigh* apparently one cannot find anything related to Galaxy, at least since 
> the term Galaxy got "hijacked" by the smartphone of the same name ;)

Please use these URL for searching:

http://galaxyproject.org/search/web/

Cheers,
Bjoern

>
> Thanks,
> Manuel
> ________________________________________
> From: Björn Grüning [bjoern.gruen...@pharmazie.uni-freiburg.de]
> Sent: Wednesday, April 10, 2013 11:37 PM
> To: Holtgrewe, Manuel
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] "Local install" of Galaxy Tool
>
> Hi Manuel,
>
> is your XML file also under ${galaxy_root}/tools/${category}/ ? It
> should be.
>
> Tata,
> Bjoern
>
> > Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my 
> > binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY. 
> > However, it is not found using if the <command> tag looks as follows:
> >
> > <command>BINARY (arguments)</command>
> >
> > When I put the following, it works:
> >
> > <command>$__root_dir__/tools/CATEGORY/BINARY</command>
> >
> > Am I doing something wrong? Is there a preferable way to such a "local" 
> > installation than my second try?
> >
> > Thanks!
> > Manuel
> >
> > [1] http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial
> > ___________________________________________________________
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>
>



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