Thanks Peter, you're correct -- I've added this in 9460:da5a5077ef1e.

On Wed, Apr 17, 2013 at 10:49 AM, Peter Cock p.j.a.cock@googlemail.comwrote:

Hello all,

I recently tried adding a <version_command> tag as follows,

<version_command interpreter="python">
  blastxml_to_top_descr.py --version
</version_command>

This kind of white space is tolerated in the <version> tag, so should work here too I think. However, it resulting the Galaxy attempting to run 'python' (which stalled as there was no user input), and then 'blastxml_to_top_descr.py --version'.

The following simple change fixes this bug. In the meantime, I have used the workaround to removing the white space in the XML file:

<version_command interpreter="python">blastxml_to_top_descr.py

--version</version_command>

Could someone please test this and commit it to the trunk,

Regards,

Peter

--

$ hg diff diff -r 94e890fea3a4 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Apr 17 15:03:12 2013 +0100 +++ b/lib/galaxy/tools/__init__.py Wed Apr 17 15:45:53 2013 +0100 @@ -1094,7 +1094,7 @@ self.version_string_cmd = None version_cmd = root.find("version_command") if version_cmd is not None:

•        self.version_string_cmd = version_cmd.text
  

•        self.version_string_cmd = version_cmd.text.strip()
         version_cmd_interpreter = version_cmd.get( "interpreter",
  

None ) if version_cmd_interpreter: executable = self.version_string_cmd.split()[0] ___________________________________________________________ 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/

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