Re: [galaxy-dev] Galaxy server broken with install of latest changes
My apologies to everyone. This turns out to be a false alarm. The problem was caused by a strange, intermittent issue with the DNS servers on our campus (I'll spare you the gory details). The problem boiled down to python on my server not being able to find http://eggs.galaxyproject.org. On Aug 12, 2014, at 13:13 , Tony Kusalik kusa...@cs.usask.ca wrote: Hi, I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up. I am hoping someone can point me to the source of the problem and/or a fix. This morning my Galaxy server was running just fine. I did a hg incoming and was told that a fair number of changes were waiting to be applied, changeset 13772 through changeset 14309. Fine. I did hg pull -u and got searching for changes adding changesets adding manifests adding file changes added 538 changesets with 1738 changes to 542 files 473 files updated, 0 files merged, 152 files removed, 0 files unresolved Fine. However, now my Galaxy server will not start up and run. On sh run.sh --daemon the server dies with the following produced in paster.log where /birl2/Galaxy/galaxy-dist is the name of the installation directory. -- begin paster.log -- Traceback (most recent call last): File ./scripts/paster.py, line 33, in module serve.run() File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 10 49, in run invoke(command, command_name, options, args[1:]) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 10 55, in invoke exit_code = runner.run(args) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 22 0, in run result = self.command() File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 64 3, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 374, in loadobj global_conf=global_conf) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 399, in loadcontext global_conf=global_conf) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 561, in get_context section) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 620, in _context_from_explicit value = import_string(found_expr) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 125, in import_string return pkg_resources.EntryPoint.parse(x= + s).load(False) File /birl2/Galaxy/galaxy-dist/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /birl2/Galaxy/galaxy-dist/lib/galaxy/web/__init__.py, line 4, in modul e from framework import expose File /birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py, line 48 , in module eggs.require( amqp ) File /birl2/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 414, in req uire raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) galaxy.eggs.EggNotFetchable: ['amqp'] Removing PID file paster.pid -- end paster.log -- The above is the complete content of paster.log. Anyone have any idea what the problem is? More importantly, how do I fix the problem and get Galaxy running again? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] 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. ___ 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
Re: [galaxy-dev] problem with bioc_qvalue, Version: 1.34.0
Thanks for the response. I have made some progress, but I don't seem to be out-of-the-woods yet. I realized that when I had invoked sh ./scripts/migrate_tools/0010_tools.sh I had done it as root, rather than as user galaxy. Hence I did a chmod -R galaxy:galaxy on both the shed_tools/ and tool_dependencies/ directories. Then in the Galaxy Admin interface I selected the Installed tool shed repositories option. I clicked on update tool shed status in the upper right corner. I waited for that update to complete. About 15 lines down the window is the line for compute_q_values. It's installation status was given as Installed, missing tool dependencies. At the very left, it was marked with a green check mark (This is the latest installable revision of this repository) and an attention symbol (Updates are available in the Tool Shed for this revision). I choose get updates from the pull-down menu associated with compute_q_values. The update window appeared, and I toggled on Install. The installation SEEMED to be okay. Now I went back to the Installed tool shed repositories window. compute_q_values was marked with just a green check mark. The revision column/field is given as 62f7b9c20c9b. The only problem is that the Installation Status is still marked with Installed, missing tool dependencies. Looking at the last 100 or so lines of paster.log, it appears that the install of compute_q_values was indeed successful. Nothing about missing dependencies reported there. Selecting update tool shed status does not change anything. Suggestions? Should I try running sh ./scripts/migrate_tools/0010_tools.sh again? Or might that just make matters worse? On 2014-04-22, at 7:56 , Dave Bouvier d...@bx.psu.edu wrote: David, Tony, I have not yet been able to reproduce the behavior you've reported here. I will continue to investigate, but if you go to Manage installed tool shed repositories in your Galaxy admin interface and select the Update tool shed status option on the compute_q_values repository, your Galaxy instance should detect that there is an update available and give you the option to update the repository and install its dependencies. Your report did help me uncover a potentially related issue with determining dependencies of repositories that have been updated after being added to the migrate_tools definition, which has now been resolved. --Dave B. On 04/17/2014 04:35 PM, David Hoover wrote: I saw the same phenomenon. I think it stems from the current version of compute_q_values pointing to unavailable revisions of both R and the bioc_qvalue R package. Whoever maintains the compute_q_values needs to straighten out the revision ids. David Hoover Helix Systems Staff National Institutes of Health On Apr 17, 2014, at 1:38 PM, Tony Kusalik kusa...@cs.usask.ca wrote: Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with bioc_qvalue or 11735242a19e but nothing was turned up. Tony Kusalik ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] problem with bioc_qvalue, Version: 1.34.0
Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with bioc_qvalue or 11735242a19e but nothing was turned up. Tony Kusalik ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] problem with bioc_qvalue, Version: 1.34.0
Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with bioc_qvalue or 11735242a19e but nothing was turned up. Tony Kusalik ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
