please help! our install of galaxy is completely unable to load any data into libraries now!
URL: http://galaxy.jgi-psf.org/library_common/act_on_multiple_datasets?library_id... File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/controllers/library_common.py', line 1384 in act_on_multiple_datasets archive.add( ldda.dataset.file_name, path ) UnboundLocalError: local variable 'archive' referenced before assignment
i tried adding a new library to see if i could see it but i get an error symlinking or copying from filesystem paths:
Miscellaneous information: Traceback (most recent call last): File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 326, in __main__() File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in __main__ a error
I could upload, but I still get the first error
Thanks in advance for any assistance! Ed Kirton
Ed, what Galaxy rev are you running? You can find this out by typing "hg heads" in your Galaxy root directory.
On Mar 16, 2010, at 3:52 PM, Edward Kirton wrote:
please help! our install of galaxy is completely unable to load any data into libraries now!
URL: http://galaxy.jgi-psf.org/library_common/act_on_multiple_datasets?library_id... File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/controllers/library_common.py', line 1384 in act_on_multiple_datasets archive.add( ldda.dataset.file_name, path ) UnboundLocalError: local variable 'archive' referenced before assignment
i tried adding a new library to see if i could see it but i get an error symlinking or copying from filesystem paths:
Miscellaneous information: Traceback (most recent call last): File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 326, in __main__() File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in __main__ a error
I could upload, but I still get the first error
Thanks in advance for any assistance! Ed Kirton
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi Greg, I'm using the latest galaxy-dist: changeset: 3511:44e9b5ca9cf0 tag: tip user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 21:01:20 2010 -0500 summary: Remove deprecated rgenetics Lmap datatype from datatypes_conf.xml.sample
On Tue, Mar 16, 2010 at 1:09 PM, Greg Von Kuster greg@bx.psu.edu wrote:
Ed, what Galaxy rev are you running? You can find this out by typing "hg heads" in your Galaxy root directory.
On Mar 16, 2010, at 3:52 PM, Edward Kirton wrote:
please help! our install of galaxy is completely unable to load any data into libraries now!
URL: http://galaxy.jgi-psf.org/library_common/act_on_multiple_datasets?library_id... '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/controllers/library_common.py', line 1384 in act_on_multiple_datasets archive.add( ldda.dataset.file_name, path ) UnboundLocalError: local variable 'archive' referenced before assignment
i tried adding a new library to see if i could see it but i get an error symlinking or copying from filesystem paths:
Miscellaneous information:Traceback (most recent call last): File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 326, in __main__() File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in __main__ a error
I could upload, but I still get the first error
Thanks in advance for any assistance! Ed Kirton
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi Ed,
This is fixed in r3539, which is not on galaxy-dist yet but is on galaxy-central (http://bitbucket.org/galaxy/galaxy-central/changeset/4a670e8f4248/)
Kanwei
On Tue, Mar 16, 2010 at 4:42 PM, Edward Kirton ESKirton@lbl.gov wrote:
Hi Greg, I'm using the latest galaxy-dist: changeset: 3511:44e9b5ca9cf0 tag: tip user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 21:01:20 2010 -0500 summary: Remove deprecated rgenetics Lmap datatype from datatypes_conf.xml.sample
On Tue, Mar 16, 2010 at 1:09 PM, Greg Von Kuster greg@bx.psu.edu wrote:
Ed, what Galaxy rev are you running? You can find this out by typing "hg heads" in your Galaxy root directory. On Mar 16, 2010, at 3:52 PM, Edward Kirton wrote:
please help! our install of galaxy is completely unable to load any data into libraries now! URL: http://galaxy.jgi-psf.org/library_common/act_on_multiple_datasets?library_id... File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/controllers/library_common.py', line 1384 in act_on_multiple_datasets archive.add( ldda.dataset.file_name, path ) UnboundLocalError: local variable 'archive' referenced before assignment i tried adding a new library to see if i could see it but i get an error symlinking or copying from filesystem paths: Miscellaneous information:Traceback (most recent call last): File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 326, in __main__() File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in __main__ a error I could upload, but I still get the first error Thanks in advance for any assistance! Ed Kirton _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hello, I replaced the offending file with the version from galaxy-central branch and the problem went away. Thank you very much. Ed
On Mar 16, 2010, at 2:40 PM, Kanwei Li wrote:
Hi Ed,
This is fixed in r3539, which is not on galaxy-dist yet but is on galaxy-central (http://bitbucket.org/galaxy/galaxy-central/changeset/4a670e8f4248/)
Kanwei
On Tue, Mar 16, 2010 at 4:42 PM, Edward Kirton ESKirton@lbl.gov wrote:
Hi Greg, I'm using the latest galaxy-dist: changeset: 3511:44e9b5ca9cf0 tag: tip user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 21:01:20 2010 -0500 summary: Remove deprecated rgenetics Lmap datatype from datatypes_conf.xml.sample
On Tue, Mar 16, 2010 at 1:09 PM, Greg Von Kuster greg@bx.psu.edu wrote:
Ed, what Galaxy rev are you running? You can find this out by typing "hg heads" in your Galaxy root directory. On Mar 16, 2010, at 3:52 PM, Edward Kirton wrote:
please help! our install of galaxy is completely unable to load any data into libraries now! URL: http://galaxy.jgi-psf.org/library_common/act_on_multiple_datasets?library_id... File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/controllers/library_common.py', line 1384 in act_on_multiple_datasets archive.add( ldda.dataset.file_name, path ) UnboundLocalError: local variable 'archive' referenced before assignment i tried adding a new library to see if i could see it but i get an error symlinking or copying from filesystem paths: Miscellaneous information:Traceback (most recent call last): File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 326, in __main__() File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in __main__ a error I could upload, but I still get the first error Thanks in advance for any assistance! Ed Kirton _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev@lists.galaxyproject.org
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Edward Kirton -
Edward Kirton
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Greg Von Kuster -
Kanwei Li