Question: Problem With <Version_Command> Xml Tag
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gravatar for Greg Edwards
6.8 years ago by
Greg Edwards190
Greg Edwards190 wrote:
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.3Cversi on_command.3E_tag_set still references "<version_string>" instead of "<version_command>". I see from a search of source code commits this name change was made in July 2011. ) Thanks ! Greg E -- Greg Edwards gedwards2@gmail.com
galaxy • 702 views
ADD COMMENTlink modified 6.8 years ago by Peter Cock1.4k • written 6.8 years ago by Greg Edwards190
0
gravatar for Peter Cock
6.8 years ago by
Peter Cock1.4k
European Union
Peter Cock1.4k wrote:
of Galaxy. galaxy/tools/myTools/myPerlTool.xml needs to have a full pathname. -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 as the main run. http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cversi on_command.3E_tag_set still references "<version_string>" instead of "<version_command>". I see from a search of source code commits this name change was made in July 2011. ) See also: https://bitbucket.org/galaxy/galaxy-central/issue/688/ Peter
ADD COMMENTlink written 6.8 years ago by Peter Cock1.4k
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