Hi guys, I found that the problematic loc files were created by CloudBioLinux and point to the reference indexes downloaded by CloudBioLinux script. I suspect that Manage Local Data cannot recognize the file structure created by CloudBioLinux?
Anyhow, I removed all the loc files from CloudBioLinux, then Manage Local Data can run now. Soon after I tried to download the bowtie hg18 from ucsc, I was given another error caused by "deferred job queue": URL: http://129.94.136.11:8080/galaxy_dev/data_admin/download_build File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/controllers/data_admin.py', line 199 in download_build jobid = trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].create_job( trans, url, dbkey, longname, indexers ) AttributeError: 'JobManager' object has no attribute 'deferred_job_queue' Anyone can give some hints about what was going on? Regards, Derrick On Fri, Sep 7, 2012 at 4:26 PM, Derrick Lin <klin...@gmail.com> wrote: > Hi guys, > > I enabled the tool with enable_beta_job_managers = True, server runs > fine. But after I clicked on Manage local data, it gave the following error: > > URL: http://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data > [^<http://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data> > ] > File > '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', > line 364 in respond > app_iter = self.application(environ, detect_start_response) > File > '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', > line 98 in __call__ > environ, self.app) > File > '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', > line 539 in intercept_output > app_iter = application(environ, replacement_start_response) > File > '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', > line 80 in __call__ > return self.application(environ, start_response) > File > '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File > '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/base.py', > line 160 in __call__ > body = method( trans, **kwargs ) > File > '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/__init__.py', > line 184 in decorator > return func( self, trans, *args, **kwargs ) > File > '/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/controllers/data_admin.py', > line 47 in manage_data > genomes[ dbkey ][ table ] = dict( state='Generated', > style=self.jobstyles[ 'done' ] ) > KeyError: 'phix' > > I tried to fix it by commenting out all the phix entries in all .loc > files. Then it gave the same error but this time caused by "hg18". I think > it must have something to do with builts.txt, manual_builts.txt and the loc > files? > > Thanks > Derrick >
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