Hi, After a crash recovery and a second trial I must admit that I cannot upgrade our galaxy instance. I need some help...
the facts: initial instance: $ hg head changeset: 8796:961ae35ba612 branch: stable tag: tip parent: 8794:1c7174911392 user: Nate Coraor <n...@bx.psu.edu> date: Fri Feb 08 11:23:04 2013 -0500 summary: Added tag release_2013.02.08 for changeset 1c7174911392 changeset: 8795:9fd7fe0c5712 parent: 8785:25bd9d387135 parent: 8794:1c7174911392 user: Nate Coraor <n...@bx.psu.edu> date: Fri Feb 08 11:22:54 2013 -0500 summary: merge from stable Then I pull the upgrade using mercurial and update the postgresql database as follows: $ hg pull pulling from https://bitbucket.org/galaxy/galaxy-dist/ searching for changes adding changesets adding manifests adding file changes added 516 changesets with 1568 changes to 710 files (-1 heads) (run 'hg update' to get a working copy) galaxy@GED-Server:~/galaxy-dist$ hg update release_2013.04.01 merging lib/galaxy/web/form_builder.py merging tools/ngs_rna/tophat_wrapper.xml 750 files updated, 2 files merged, 433 files removed, 0 files unresolved galaxy@GED-Server:~/galaxy-dist$ hg branch stable galaxy@GED-Server:~/galaxy-dist$ sh manage_db.sh upgrade 110 -> 111... Add support for job destinations to the job table done 111 -> 112... Migration script to add the data_manager_history_association table and data_manager_job_association. 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-04-16 00:59:22,412 Created data_manager_history_association table 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-04-16 00:59:22,412 Created data_manager_history_association table 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-04-16 00:59:22,428 Created data_manager_job_association table 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-04-16 00:59:22,428 Created data_manager_job_association table done 112 -> 113... Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. done 113 -> 114... Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. done When I restarts the server, I have $ sh run.sh --reload Initializing data_manager_conf.xml from data_manager_conf.xml.sample Initializing shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample Some eggs are out of date, attempting to fetch... Fetched http://eggs.galaxyproject.org/PasteDeploy/PasteDeploy-1.5.0-py2.7.egg Removed conflicting egg: /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg Fetch successful. > I suspect that some new python eggs may cause my troubles... and then, ... some usual bla bla... and finishes by .... galaxy.webapps.galaxy.buildapp DEBUG 2013-04-16 01:00:30,077 Enabling 'Request ID' middleware Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1056, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1062, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 227, in run result = self.command() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 650, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj return context.create() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create return self.object_type.invoke(self) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 332, in invoke filtered = context.next_context.create() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create return self.object_type.invoke(self) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 172, in app_factory webapp = wrap_in_static( webapp, global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 327, in wrap_in_static urlmap["/static"] = Static( conf.get( "static_dir" ), cache_time ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/static.py", line 16, in __init__ StaticURLParser.__init__( self, directory ) File "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/urlparser.py", line 430, in __init__ self.directory = self.normpath(directory) File "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/urlparser.py", line 435, in normpath return os.path.normcase(os.path.abspath(path)) File "/usr/lib/python2.7/posixpath.py", line 343, in abspath if not isabs(path): File "/usr/lib/python2.7/posixpath.py", line 53, in isabs return s.startswith('/') *AttributeError: 'NoneType' object has no attribute 'startswith'* *galaxy.jobs.handler INFO 2013-04-16 01:00:30,112 sending stop signal to worker thread* *galaxy.jobs.handler INFO 2013-04-16 01:00:30,112 job handler queue stopped* *galaxy.jobs.runners INFO 2013-04-16 01:00:30,112 LWRRunner: Sending stop signal to monitor thread* *galaxy.jobs.runners INFO 2013-04-16 01:00:30,112 LWRRunner: Sending stop signal to 3 worker threads* *galaxy.jobs.runners INFO 2013-04-16 01:00:30,113 LocalRunner: Sending stop signal to 5 worker threads* *galaxy.jobs.handler INFO 2013-04-16 01:00:30,115 sending stop signal to worker thread* *galaxy.jobs.handler INFO 2013-04-16 01:00:30,115 job handler stop queue stopped* does anyone has a clue about what is going wrong (eggs or something...) Thanks thanks thanks in advance.... -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org
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