errors with startup of galaxy server
Hi, On April 16th, I did an hg incoming command to update my local version of Galaxy. Once I restarted my server, I was told to do sh ./scripts/migrate_tools/0010_tools.sh take care of tools which had been migrated to the tool shed. Ever since the two changes above, I am seeing strange errors in paster.log that I do not understand. Here are some samples: (Note that Galaxy is installed in directory /birl2/Galaxy.) -- begin paste -- galaxy.tools ERROR 2014-04-23 12:29:48,869 Error reading tool from path: data_source/bx_browser.xml Traceback (most recent call last): File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658, in load_tool tree = load_tool( config_file ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' galaxy.tools ERROR 2014-04-23 12:29:48,921 Error reading tool from path: data_source/flymine.xml Traceback (most recent call last): File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658, in load_tool tree = load_tool( config_file ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' galaxy.tools ERROR 2014-04-23 12:29:48,921 Error reading tool from path: data_source/flymine_test.xml Traceback (most recent call last): File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658, in load_tool tree = load_tool( config_file ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") -- end paste -- This pattern of error messages continues for/from flymine_test.xml, mousemine.xml, ratmine.xml, yeastmine.xml, metabolicmine.xml, encode_db.xml, epigraph_import.xml, epigraph_import_test.xml, epigraph.xml, epigraph_test.xml, gencode_partition.xml, random_intervals.xml, column_join.xml, wiggle_to_simple, phastOdds_tool.xml. The general theme is the constant reference to "elementtree-1.2.6_20050316-py2.7.egg". Also of note is that an ls command says that /birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg is a regular file, and not a directory. Within the Galaxy Admin window, I tried to search for tools (either installed or available) matching "ElementTree" but couldn't find anything. Further, checking paster.log files from prior to having given the sh ./scripts/migrate_tools/0009_tools.sh command, I see /birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg mentioned in the python path given at the beginning of paster.log, but no error messages involving "ElementTree" or "elementtree". How do I deal with this problem, and get the server to come up error free? Any suggestions would be welcome.
Hi Tony, this is side-effect of tool migration and should not effect how Galaxy runs in any way. Please ignore it for now, we will fix it later. :) thanks Martin On Wed, Apr 23, 2014 at 5:55 PM, Tony Kusalik <kusalik@cs.usask.ca> wrote:
Hi,
On April 16th, I did an hg incoming command to update my local version of Galaxy. Once I restarted my server, I was told to do sh ./scripts/migrate_tools/0010_tools.sh take care of tools which had been migrated to the tool shed.
Ever since the two changes above, I am seeing strange errors in paster.log that I do not understand. Here are some samples: (Note that Galaxy is installed in directory /birl2/Galaxy.)
-- begin paste -- galaxy.tools ERROR 2014-04-23 12:29:48,869 Error reading tool from path: data_source/bx_browser.xml Traceback (most recent call last): File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658, in load_tool tree = load_tool( config_file ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' galaxy.tools ERROR 2014-04-23 12:29:48,921 Error reading tool from path: data_source/flymine.xml Traceback (most recent call last): File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658, in load_tool tree = load_tool( config_file ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' galaxy.tools ERROR 2014-04-23 12:29:48,921 Error reading tool from path: data_source/flymine_test.xml Traceback (most recent call last): File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658, in load_tool tree = load_tool( config_file ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") -- end paste --
This pattern of error messages continues for/from flymine_test.xml, mousemine.xml, ratmine.xml, yeastmine.xml, metabolicmine.xml, encode_db.xml, epigraph_import.xml, epigraph_import_test.xml, epigraph.xml, epigraph_test.xml, gencode_partition.xml, random_intervals.xml, column_join.xml, wiggle_to_simple, phastOdds_tool.xml. The general theme is the constant reference to "elementtree-1.2.6_20050316-py2.7.egg". Also of note is that an ls command says that /birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg is a regular file, and not a directory.
Within the Galaxy Admin window, I tried to search for tools (either installed or available) matching "ElementTree" but couldn't find anything. Further, checking paster.log files from prior to having given the sh ./scripts/migrate_tools/0009_tools.sh command, I see /birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg mentioned in the python path given at the beginning of paster.log, but no error messages involving "ElementTree" or "elementtree".
How do I deal with this problem, and get the server to come up error free? Any suggestions would be welcome.
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participants (2)
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Martin Čech -
Tony Kusalik