Hi, I'm in the process of adding a proteomics Perl script into a local copy of Galaxy. It seems like the version command in the galaxy/tools/myTools/myPerlTool.xml needs to have a full pathname. The doco indicates this should be enough: <version_command>myPerlTool -version</version_command>, and the few examples of it's use in galaxy/tools/*/*.xml are not full path, but on my installation this gives, in the Tool Version section of the View Details page of the run result /bin/sh: myPerlTool.pl: command not found I was expecting the version command to pick up the same path/environment as the main run. (Also, trivia dept, the doco in http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cversion_com... still references "<version_string>" instead of "<version_command>". I see from a search of source code commits this name change was made in July

On Tuesday, January 3, 2012, Greg Edwards <gedwards2@gmail.com> wrote: 2011. )

Thanks ! Greg E

See also: https://bitbucket.org/galaxy/galaxy-central/issue/688/ Peter