Peter, Thank you so much for the help
Date: Thu, 25 Apr 2013 18:35:33 +0100 Subject: Re: [galaxy-dev] /bin/sh: 1: filename: not found From: p.j.a.cock@googlemail.com To: ramao_tiago_tiburski@hotmail.com CC: galaxy-dev@lists.bx.psu.edu
On Thu, Apr 25, 2013 at 5:37 PM, Ramon Tiburski <ramao_tiago_tiburski@hotmail.com> wrote:
Hi Peter,
I have this: <command>filename $input $output</command>
And my executable and xml are in the same directory
Thank you
If you don't put the binary on the system $PATH, then you'll need to give an explicit path to it. You could try something like this in the short term while you are developing the tool:
<command>/mnt/galaxy/tools/my_stuff/filename $input $output</command>
If you intend to share this tool then you'll need to learn about how automatic dependency installation works via a tool_dependencies.xml file.
Peter