I created a new tool in c++, and the "filename" is the name of my executable file. I have the xml and the executable file in the same directory, but I get this error when I try to run the tool. Someone can help me with this error? Thank you
On Thu, Apr 25, 2013 at 5:25 PM, Ramon Tiburski <ramao_tiago_tiburski@hotmail.com> wrote:
I created a new tool in c++, and the "filename" is the name of my executable file. I have the xml and the executable file in the same directory, but I get this error when I try to run the tool. Someone can help me with this error?
Thank you
Please show us the (start of) your tool's XML file, in particular the <command> tag. My guess is you have something like this: <command>filename arg1 arg2</command> Unless your executable is on the path that won't work. Peter
Hi Peter, I have this: <command>filename $input $output</command> And my executable and xml are in the same directory Thank you
Date: Thu, 25 Apr 2013 17:29:35 +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 5:25 PM, Ramon Tiburski <ramao_tiago_tiburski@hotmail.com> wrote:
I created a new tool in c++, and the "filename" is the name of my executable file. I have the xml and the executable file in the same directory, but I get this error when I try to run the tool. Someone can help me with this error?
Thank you
Please show us the (start of) your tool's XML file, in particular the <command> tag.
My guess is you have something like this:
<command>filename arg1 arg2</command>
Unless your executable is on the path that won't work.
Peter
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
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
participants (2)
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Peter Cock -
Ramon Tiburski