Hi Greg
Thank you very much for you help.
I managed to fix '~/lib/galaxy/tools/__init__.py' manually according
the diff in your changeset, and it is working fine.
Regards, Hans
On 08/16/2011 05:01 PM, Greg Von Kuster wrote:
Hans,
This bug was fixed in the following change set - not sure if it is currently
available in the distribution. If not, it should be within the next few weeks.
If you need it sooner, you'll have to pull from our development repo at
http://bitbucket.org/galaxy/galaxy-central/
0f15591f2acd Fix for tool configs that do not include a command tag.
Branch
25 days ago
On Aug 16, 2011, at 10:38 AM, Hans-Rudolf Hotz wrote:
Hi
I apologize, if this problem has already been solved/discussed. I went through
the e-mail repos, but couldn't find anything.
With a little delay, I am in the process of upgrading our local Galaxy server. Currently,
I am running a few tests with the "June 23, 2011 (720455407d1c)" release.
I noticed the following problem during start-up of a fresh download:
galaxy.tools DEBUG 2011-08-16 16:15:06,567 Loading section: SNP/WGA: Data;
Filters
galaxy.tools DEBUG 2011-08-16 16:15:06,630 Loaded tool: upload1 1.1.3
galaxy.tools ERROR 2011-08-16 16:15:06,639 error reading tool from path:
data_source/access_libraries.xml
Traceback (most recent call last):
File "/galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py", line 77,
in load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py", line
169, in load_tool
return ToolClass( config_file, root, self.app )
File "/galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py", line
340, in __init__
self.parse( root )
File "/galaxy/galaxy_test/galaxy_dist/lib/galaxy/tools/__init__.py", line
385, in parse
self.interpreter = command.get("interpreter", None)
AttributeError: 'NoneType' object has no attribute 'get'
galaxy.tools DEBUG 2011-08-16 16:15:06,687 Loaded tool: rgClean1 1.0.0
and as a consequence: the tool "Access Libraries stored locally" is not available. Does
anybody know, what went wrong? - The "__init__.py" is a little bit too big of a beast
for me ;)
We use this tool quite a lot for general access to data libraries (in addition
to the drop down in the top menu bar)
Thank you very much for any help
Regards, Hans
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Greg Von Kuster
Galaxy Development Team
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