[galaxy-dev] /bin/sh: 1: filename: not found
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 keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] /bin/sh: 1: filename: not found
On Thu, Apr 25, 2013 at 5:25 PM, Ramon Tiburski ramao_tiago_tibur...@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: commandfilename arg1 arg2/command Unless your executable is on the path that won't work. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] /bin/sh: 1: filename: not found
Hi Peter, I have this: commandfilename $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.c...@googlemail.com To: ramao_tiago_tibur...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu On Thu, Apr 25, 2013 at 5:25 PM, Ramon Tiburski ramao_tiago_tibur...@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: commandfilename arg1 arg2/command Unless your executable is on the path that won't work. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] /bin/sh: 1: filename: not found
On Thu, Apr 25, 2013 at 5:37 PM, Ramon Tiburski ramao_tiago_tibur...@hotmail.com wrote: Hi Peter, I have this: commandfilename $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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] /bin/sh: 1: filename: not found
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.c...@googlemail.com To: ramao_tiago_tibur...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu On Thu, Apr 25, 2013 at 5:37 PM, Ramon Tiburski ramao_tiago_tibur...@hotmail.com wrote: Hi Peter, I have this: commandfilename $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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
