problems with "Access Libraries stored locally" tool
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
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 ___________________________________________________________ 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
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 ___________________________________________________________ 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
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Hans-Rudolf Hotz