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