Path to tool designation in tool config xml
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. Timothy
On Tue, Sep 6, 2011 at 9:41 AM, Timothy Wu <2huggie@gmail.com> 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.
Timothy
Normally on a Unix/Linux system you'd just put the tool on the path (or add the tool's location to the system path). Peter
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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Thanks, this helps. I was running with an interpreter and I didn't realize I had to had the full path in there. I was expecting that $PATH which contains the directory the script was located in to take care of it. Thanks you very much for the clarification. Timothy
Timothy Wu wrote:
Thanks, this helps. I was running with an interpreter and I didn't realize I had to had the full path in there. I was expecting that $PATH which contains the directory the script was located in to take care of it. Thanks you very much for the clarification.
If the script is executable and in your $PATH and has the proper #! line at the top, you don't need 'interpreter='. --nate
Timothy
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participants (3)
-
Nate Coraor -
Peter Cock -
Timothy Wu