Hi Chris,

Actually, I tried originally to call my programs in that way and galaxy gave me messages like this

/path/to/my/tool: /path/to/my/tool: cannot execute binary file

But now I tried once more and I have just realised that I forgot to delete the 'interpreter="sh"' ;-) Now it works! Thanks for the heads up!

cheers, Erick

Hi Erick,

You give paths to the scripts/binaries in the XML file e.g.:

<command interpreter="sh">/path/to/my_script.sh -p1 $p1 -p2 $p2 -p3 $p3</command>

Or you can use environment variables like $PATH or $BLASTDIR. So, there's no need for the tool to be in the same directory at all. Cheers,

Chris

Erick Antezana wrote:

...

Hi,

while defining my own XML tool (.../galaxy/tools/my_tool.xml) I need, apparently?, to have a copy of the tool in the same location so that the XML section dedicated to call the command could find it (my_script.sh):

<command interpreter="sh">my_script.sh -p1 $p1 -p2 $p2 -p3 $p3</command>

is there a way to avoid such situation withou creating a wrapper and calling directly the tool/script? If I want to make a call to programs like blast, srs, etc, it won't be wise to have a copy of them in that location... For the moment, I created a simple shell script that actually calls the program required witht the arguments coming from galaxy...

thanks, Erick

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