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

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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

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

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