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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