Hi Manuel,

collect your binaries in a separate location and add to PATH and your
cluster. If you want to ship your tool in the toolshed, the installation
and PATH will be automatically added once you installed it from the
toolshed. Have a look at:

http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories

Regards,
Bjoern

> 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
> > > ___________________________________________________________
> > > Please keep all replies on the list by using "reply all"
> > > in your mail client.  To manage your subscriptions to this
> > > and other Galaxy lists, please use the interface at:
> > >   http://lists.bx.psu.edu/
> > >
> > > To search Galaxy mailing lists use the unified search at:
> > >   http://galaxy
> >
> >
> 
> 


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