Hello,
We have been running a local mirror of Galaxy on our cluster for few
months now. Recently, I went ahead and updated the local repository
using "hg pull -u". After attempting to run the latest version, I found
out that SGE was updated to 6.2u5 (from 6.2u3). We compiled the
DRMAA_python egg for Galaxy, but unfortunately we are unable to access
it over the browser. The problem is that ToolRunner controller fails (as
shown below) and Galaxy is not served via http. Here's the log:
galaxy.jobs INFO 2010-04-09 13:19:28,003 job stopper started
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,056 Enabling 'admin'
controller, class: Admin
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,063 Enabling 'async'
controller, class: ASync
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,265 Enabling 'cloud'
controller, class: CloudController
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,337 Enabling
'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,342 Enabling 'error'
controller, class: Error
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,354 Enabling 'forms'
controller, class: Forms
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,367 Enabling
'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,371 Enabling
'library' controller, class: Library
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,376 Enabling
'library_admin' controller, class: LibraryAdmin
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,398 Enabling
'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,402 Enabling
'mobile' controller, class: Mobile
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,407 Enabling 'page'
controller, class: PageController
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,411 Enabling
'requests' controller, class: Requests
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,440 Enabling
'requests_admin' controller, class: RequestsAdmin
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,445 Enabling 'root'
controller, class: RootController
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,449 Enabling 'tag'
controller, class: TagsController
galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,453 Enabling
'tool_runner' controller, class: ToolRunner
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in <module>
command.run()
File
"/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/command.py", line 84, in run
invoke(command, command_name, options, args[1:])
File
"/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/command.py", line 123, in invoke
exit_code = runner.run(args)
File
"/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/command.py", line 218, in run
result = self.command()
File
"/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/serve.py", line 276, in command
relative_to=base, global_conf=vars)
File
"/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/serve.py", line 313, in loadapp
**kw)
File
"/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 204, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
"/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 225, in loadobj
return context.create()
File
"/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 625, in create
return self.object_type.invoke(self)
File
"/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 188, in invoke
filtered = context.next_context.create()
File
"/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 625, in create
return self.object_type.invoke(self)
File
"/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 110, in invoke
return fix_call(context.object, context.global_conf,
**context.local_conf)
File
"/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call
val = callable(*args, **kw)
File "/LOCATION/galaxy/lib/galaxy/web/buildapp.py", line 69, in
app_factory
add_controllers( webapp, app )
File "/LOCATION/galaxy/lib/galaxy/web/buildapp.py", line 39, in
add_controllers
module = __import__( module_name )
File "/LOCATION/galaxy/lib/galaxy/web/controllers/tracks.py", line 27,
in <module>
from galaxy.visualization.tracks.data.bam import BamDataProvider
File "/LOCATION/galaxy/lib/galaxy/visualization/tracks/data/bam.py",
line 7, in <module>
from pysam import csamtools
File
"/usr/lib/python-2.5.2/lib/python2.5/site-packages/PIL/__init__.py",
line 1, in <module>
#
File "build/bdist.linux-x86_64-ucs2/egg/pysam/csamtools.py", line 7,
in <module>
File "build/bdist.linux-x86_64-ucs2/egg/pysam/csamtools.py", line 6,
in __bootstrap__
ImportError: /HOME_LOCATION/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_64-ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader
Your help will be greatly appreciated.
Thanks,
Martin