June 21, 2010 Galaxy Development News Brief

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June 21, 2010 Galaxy Development News Brief

Greg Von Kuster
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_06_21


Greg Von Kuster
Galaxy Development Team
[hidden email]




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Trackster broken? [was: June 21, 2010 Galaxy Development News Brief]

Davide Cittaro

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_06_21


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
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
*/




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Re: Trackster broken? [was: June 21, 2010 Galaxy Development News Brief]

Kanwei Li
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
<[hidden email]> 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_06_21
>
>
> 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+Mar.+2006+(NCBI36%2Fhg18)+(hg18)
> 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: [hidden email]
> */
>
>
>
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
>

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Re: Trackster broken? [was: June 21, 2010 Galaxy Development News Brief]

Davide Cittaro
Hi Kanwei,

 Kanwei Li ([hidden email]) 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: [hidden email]
*/




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Re: Trackster broken? [was: June 21, 2010 Galaxy Development News Brief]

Kanwei Li
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 ([hidden email]) 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: [hidden email]
> */
>
>
>
>


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