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_meiMobile: +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:
>
> http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
___
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/
