Makais, 

Any type of command line tool, whether script or a binary executable, can be 
used by Galaxy as long as it's properly installed on the system and accessible 
to the Galaxy user.

See 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set
 for more details on how you might call a compiled executable.

Thanks for using Galaxy,

-Dannon

On Oct 6, 2011, at 7:44 AM, Makis Ladoukakis wrote:

> Dear Galaxy developers,
> 
> Currently I am adding new tools to my galaxy instance as scripts written in 
> Perl language. I was wandering if there is a way to add tools either as .bin 
> or .exe format or if only scripts are supported. I couldn't find anything 
> about it in the wiki or in the FAQ. 
> 
> Thank you,
> Makis Ladoukakis
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