This is due to a bug that was corrected in change set 5819:0f15591f2acd, which should be available in our main Galaxy instance, as well as the distribution, within the next few weeks. If you need it sooner, you can pull it from our development repo. Sorry for the inconvenience. Greg Von Kuster On Jul 22, 2011, at 11:00 AM, Leon Mei wrote:
Dear all,
I installed a local galaxy using the latest codebase yesterday. During the startup, the loading of 3 tool wrappers are failed: epigraph.xml, epigraph_test.xml, access_libraries.xml.
Similar errors were reported in http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01839.html
Have other people experienced the same problem? Any suggested solutions?
Thanks, Leon
==== paster.log below === ... galaxy.tools DEBUG 2011-07-22 16:02:47,084 Loaded tool: hbvar 1.0.0 galaxy.tools DEBUG 2011-07-22 16:02:47,088 Loaded tool: fix_errors 1.0.0 galaxy.tools DEBUG 2011-07-22 16:02:47,089 Loading section: Send Data galaxy.tools ERROR 2011-07-22 16:02:47,089 error reading tool from path: data_destination/epigraph.xml Traceback (most recent call last): File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 385, in parse self.interpreter = command.get("interpreter", None) AttributeError: 'NoneType' object has no attribute 'get' galaxy.tools ERROR 2011-07-22 16:02:47,090 error reading tool from path: data_destination/epigraph_test.xml Traceback (most recent call last): File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/opt/galaxy/prog/galaxy-2011-7-21/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 2011-07-22 16:02:50,556 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2011-07-22 16:02:50,587 Loaded tool: upload1 1.1.3 galaxy.tools ERROR 2011-07-22 16:02:50,587 error reading tool from path: data_source/access_libraries.xml Traceback (most recent call last): File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 385, in parse self.interpreter = command.get("interpreter", None) AttributeError: 'NoneType' object has no attribute 'get' ...
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231 ___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu