[Patch] Adding interpreter-attribute to the version_command-tag
Hi all, if we try to wrap a single script-tool, for example bismark [1], it has its own version number and should be included in <version_command>. I would like to ship bismark with the wrapper. That means that bismark is not included in PATH, but exists next to the bismark_wrapper.xml file. That isn't a problem for the <command> tag, but for the <version_command> tag, because it assumes the executed tool in PATH. Attached is a patch that adds the same <command> logic to <version_command> if a interpreter is specified. Regards, Björn [1] http://www.bioinformatics.babraham.ac.uk/projects/bismark/
Looks great, committed in -central changeset 02fe49c3d251 Best, J. On Oct 6, 2012, at 6:31 PM, Björn Grüning wrote:
Hi all,
if we try to wrap a single script-tool, for example bismark [1], it has its own version number and should be included in <version_command>. I would like to ship bismark with the wrapper. That means that bismark is not included in PATH, but exists next to the bismark_wrapper.xml file. That isn't a problem for the <command> tag, but for the <version_command> tag, because it assumes the executed tool in PATH. Attached is a patch that adds the same <command> logic to <version_command> if a interpreter is specified.
Regards, Björn
[1] http://www.bioinformatics.babraham.ac.uk/projects/bismark/ <version_command_interpreter.patch>___________________________________________________________ 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:
participants (2)
-
Björn Grüning -
Jeremy Goecks