[galaxy-dev] Path to tool designation in tool config xml

Nate Coraor nate at bx.psu.edu
Tue Sep 6 11:39:34 EDT 2011


Timothy Wu wrote:
> Hi,
> 
> I'm trying the add tool tutorial at
> http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial . It works, but
> how do I designate the path of the tool if it's not dropped into the same
> directory as the tool config xml? Some executable may not be in the
> directory. Surely it couldn't possiblely be the case with external tools
> like BLAST, isn't it?! But looking at the BLAST config xmls I couldn't make
> out the difference and I didn't find any documentation on how to designate
> the path of the tool. Help appreciated, thank you.

Hi Timothy,

If the <command interpreter="python">command.py args...</command> tag is
used in your tool config, the command line will be assembled as:

    python /absolute/path/to/directory/containing/tool.xml/command.py args...

In this case, the interpreter (python) is expected to be found on the
$PATH.

If no interpreter is specified, i.e. <command>binary args...</command>
then `binary` is expected to be found on the $PATH.

Hope this helps,
--nate

> 
> Timothy

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