June 21, 2010 Galaxy Development News Brief
The latest news brief is available at the following link. You are strongly encouraged to upgrade to the revision detailed in this news brief as it contains important security fixes for data libraries. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_0... Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
On Jun 22, 2010, at 4:07 PM, Greg Von Kuster wrote:
The latest news brief is available at the following link. You are strongly encouraged to upgrade to the revision detailed in this news brief as it contains important security fixes for data libraries.
http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_0...
I see trackster now can take info about chroms from 2bit files (if specified in the proper .loc file)... I have both .len files (because I used to play with trackster) and .2bit files (specified before using trackster...) but get an error everytime I create a new trackster session: Could not load chroms for this dbkey The web log says: 85.239.176.228 - - [23/Jun/2010:14:24:32 +0200] "GET /tracks/chroms?dbkey=Human+Mar.+2006+(NCBI36%2Fhg18)+(hg18) HTTP/1.1" 500 - "http://host001.instruments.ifom-ieo-campus.it:8080/tracks" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.16 (KHTML, like Gecko) Version/5.0 Safari/533.16" Error - <type 'exceptions.ValueError'>: need more than 0 values to unpack URL: http://host001.instruments.ifom-ieo-campus.it:8080/tracks/chroms?dbkey=Human...) File '/data/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 '/data/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/data/galaxy_dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 103 in __call__ return self.app( environ, start_response ) File '/data/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/data/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/data/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 63 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/data/galaxy_dist/lib/galaxy/web/controllers/tracks.py', line 186 in chroms if self.available_genomes is None: self._init_references(trans) File '/data/galaxy_dist/lib/galaxy/web/controllers/tracks.py', line 104 in _init_references key, path = line.split() ValueError: need more than 0 values to unpack [cut] WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x41e1d90> paste.cookies: (<SimpleCookie: __utma='113557983.3551959740507082000.1241708833.1259073318.1265196708.48' __utmz='113557983.1265196708.48.7.utmcsr=ieo.it|utmccn=(referral)|utmcmd=referral|utmcct=/ricerca/inglese/researchgroups.shtml' galaxysession='eb142648ac45b7701c30ab67703dc42f0155958d39aa56df8786535502903d5ca958528cf2cfe07e' hguid='91197'>, 'galaxysession=eb142648ac45b7701c30ab67703dc42f0155958d39aa56df8786535502903d5ca958528cf2cfe07e; hguid=91197; __utma=113557983.3551959740507082000.1241708833.1259073318.1265196708.48; __utmz=113557983.1265196708.48.7.utmcsr=ieo.it|utmccn=(referral)|utmcmd=referral|utmcct=/ricerca/inglese/researchgroups.shtml') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x41e1250> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xd6d390> paste.parsed_querystring: ([('dbkey', 'Human Mar. 2006 (NCBI36/hg18) (hg18)')], 'dbkey=Human+Mar.+2006+(NCBI36%2Fhg18)+(hg18)') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_query_vars: (MultiDict([('dbkey', 'Human Mar. 2006 (NCBI36/hg18) (hg18)')]), 'dbkey=Human+Mar.+2006+(NCBI36%2Fhg18)+(hg18)') wsgi process: 'Multithreaded' ------------------------------------------------------------ d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Hi Davide, You probably had an invalid entry in your twobit.loc file but either way this has been fixed in the latest commit. Thanks, Kanwei On Wed, Jun 23, 2010 at 8:38 AM, Davide Cittaro <davide.cittaro@ifom-ieo-campus.it> wrote:
On Jun 22, 2010, at 4:07 PM, Greg Von Kuster wrote:
The latest news brief is available at the following link. You are strongly encouraged to upgrade to the revision detailed in this news brief as it contains important security fixes for data libraries.
http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_0...
I see trackster now can take info about chroms from 2bit files (if specified in the proper .loc file)... I have both .len files (because I used to play with trackster) and .2bit files (specified before using trackster...) but get an error everytime I create a new trackster session: Could not load chroms for this dbkey The web log says: 85.239.176.228 - - [23/Jun/2010:14:24:32 +0200] "GET /tracks/chroms?dbkey=Human+Mar.+2006+(NCBI36%2Fhg18)+(hg18) HTTP/1.1" 500 - "http://host001.instruments.ifom-ieo-campus.it:8080/tracks" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.16 (KHTML, like Gecko) Version/5.0 Safari/533.16" Error - <type 'exceptions.ValueError'>: need more than 0 values to unpack URL: http://host001.instruments.ifom-ieo-campus.it:8080/tracks/chroms?dbkey=Human...) File '/data/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 '/data/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/data/galaxy_dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 103 in __call__ return self.app( environ, start_response ) File '/data/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/data/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/data/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 63 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/data/galaxy_dist/lib/galaxy/web/controllers/tracks.py', line 186 in chroms if self.available_genomes is None: self._init_references(trans) File '/data/galaxy_dist/lib/galaxy/web/controllers/tracks.py', line 104 in _init_references key, path = line.split() ValueError: need more than 0 values to unpack [cut] WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x41e1d90> paste.cookies: (<SimpleCookie: __utma='113557983.3551959740507082000.1241708833.1259073318.1265196708.48' __utmz='113557983.1265196708.48.7.utmcsr=ieo.it|utmccn=(referral)|utmcmd=referral|utmcct=/ricerca/inglese/researchgroups.shtml' galaxysession='eb142648ac45b7701c30ab67703dc42f0155958d39aa56df8786535502903d5ca958528cf2cfe07e' hguid='91197'>, 'galaxysession=eb142648ac45b7701c30ab67703dc42f0155958d39aa56df8786535502903d5ca958528cf2cfe07e; hguid=91197; __utma=113557983.3551959740507082000.1241708833.1259073318.1265196708.48; __utmz=113557983.1265196708.48.7.utmcsr=ieo.it|utmccn=(referral)|utmcmd=referral|utmcct=/ricerca/inglese/researchgroups.shtml') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x41e1250> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xd6d390> paste.parsed_querystring: ([('dbkey', 'Human Mar. 2006 (NCBI36/hg18) (hg18)')], 'dbkey=Human+Mar.+2006+(NCBI36%2Fhg18)+(hg18)') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_query_vars: (MultiDict([('dbkey', 'Human Mar. 2006 (NCBI36/hg18) (hg18)')]), 'dbkey=Human+Mar.+2006+(NCBI36%2Fhg18)+(hg18)') wsgi process: 'Multithreaded' ------------------------------------------------------------ d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
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Hi Kanwei, Kanwei Li (kanwei@gmail.com) wrote:
Hi Davide,
You probably had an invalid entry in your twobit.loc file but
either
way this has been fixed in the latest commit.
Just to be sure: does trackster read only twobit.loc file? In other words, are "len" files still needed? d -- /* Davide Cittaro Next Generation Sequencing and Affymetrix data analyst Cogentech - Consortium for genomic technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Yes, len are still needed. twobit is for showing of the reference genome when you're zoomed in. Kanwei On Jun 23, 2010, at 4:43 PM, Davide Cittaro wrote:
Hi Kanwei,
Kanwei Li (kanwei@gmail.com) wrote:
Hi Davide,
You probably had an invalid entry in your twobit.loc file but
either
way this has been fixed in the latest commit.
Just to be sure: does trackster read only twobit.loc file? In other words, are "len" files still needed?
d
-- /* Davide Cittaro Next Generation Sequencing and Affymetrix data analyst
Cogentech - Consortium for genomic technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
participants (3)
-
Davide Cittaro -
Greg Von Kuster -
Kanwei Li