Pushed this patch to -central. Thanks guys! https://bitbucket.org/galaxy/galaxy-central/commits/e832e466471403d54d788193... -John On Thu, Jun 19, 2014 at 11:19 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Will,
It looks like a bug to me.
This was originally added back in 2012, https://bitbucket.org/galaxy/galaxy-central/commits/02fe49c3d251
I submitted a fix for whitespace in 2013, https://bitbucket.org/galaxy/galaxy-central/commits/da5a5077ef1ebffa9e0ad903...
Looking at the current code, yes, there does appear to be a logical flaw here:
# Versioning for tools self.version_string_cmd = None version_cmd = root.find("version_command") if version_cmd is not None: 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] abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable)) command_line = self.version_string_cmd.replace(executable, abs_executable, 1) self.version_string_cmd = self.interpreter + " " + command_line
i.e. self.interpreter is used, rather than version_cmd_interpreter
Possible fix:
$ hg diff lib/galaxy/tools/__init__.py diff -r 75be6c49a65d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed May 14 22:49:44 2014 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Jun 19 17:19:18 2014 +0100 @@ -1234,7 +1234,7 @@ executable = self.version_string_cmd.split()[0] abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable)) command_line = self.version_string_cmd.replace(executable, abs_executable, 1) - self.version_string_cmd = self.interpreter + " " + command_line + self.version_string_cmd = version_cmd_interpreter + " " + command_line # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"):
Regards,
Peter
On Thu, Jun 19, 2014 at 4:21 PM, Will Holtz <wholtz@lygos.com> wrote:
The documentation for the version_command tag doesn't mention it can take an interpreter option: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cversion_comm...
I looked at the code in lib/galaxy/tools/__init__.py to see how this was implemented. I was surprised to see that if the interpreter option is passed to version_command, then the interpreter value from the command tag is used in generating the version number response. The version_command interpreter value is never used. For example, I tried the following:
<version_command interpreter="foobar">myPythonTool -v</version_command>
<command interpreter="python">myPythonTool someCheetahCode</command>
And Galaxy successfully got the version number. Is this the expected behavior?
-Will
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