Trackster error on dbkeys

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Trackster error on dbkeys

Aarthi Mohan
Hi all,

I am setting up galaxy on a server running CentOS 6.5.
I found that Trackster application hits me with an error
"Could not load chroms for this dbkey: PF3D7", when I try "add new track" from Visualization.

I am working with Plasmodium falciparum (PF3d7) genome, and I followed the instruction for setting visualization from "https://wiki.galaxyproject.org/Visualization%20Setup" and placed the 2bit, len files in the appropriate path.

I have also made sure the genome build is present in the builds.txt under tool-data/shared/ucsc.

For a test, I have the human chromosomes len files and Trackster loads it without any problem.

Any suggestion would greatly help me.

Thanks
RT

Log file:
-----------
127.0.0.1 - - [10/Apr/2014:12:29:44 +0800] "GET /visualization/trackster HTTP/1.1" 200 - "http://127.0.0.1:8081/" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
127.0.0.1 - - [10/Apr/2014:12:29:45 +0800] "GET /api/genomes?chrom_info=True HTTP/1.1" 200 - "http://127.0.0.1:8081/visualization/trackster" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
127.0.0.1 - - [10/Apr/2014:12:29:51 +0800] "GET /api/genomes/PF3D7?low=0&num=100 HTTP/1.1" 500 - "http://127.0.0.1:8081/visualization/trackster" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
Error - <type 'exceptions.IndexError'>: list index out of range
URL: http://127.0.0.1:8081/api/genomes/PF3D7?low=0&num=100
File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/data/maarthi/Galaxy/Test/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/data/maarthi/Galaxy/Test/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__
  return self.handle_request( environ, start_response )
File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request
  body = method( trans, **kwargs )
File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 78 in decorator
  return to_json_string( func( self, trans, *args, **kwargs ) )
File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/webapps/galaxy/api/genomes.py', line 42 in show
  rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low )
File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/visualization/genomes.py', line 292 in chroms
  rval = genome.to_dict( num=num, chrom=chrom, low=low )
File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/visualization/genomes.py', line 153 in to_dict
  chroms[ fields[0] ] = int( fields[1] )
IndexError: list index out of range


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'application/json, text/javascript, */*; q=0.01'
  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
  HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
  HTTP_CONNECTION: 'keep-alive'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351'
  HTTP_HOST: '127.0.0.1:8081'
  HTTP_REFERER: 'http://127.0.0.1:8081/visualization/trackster'
  HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0'
  HTTP_X_REQUESTED_WITH: 'XMLHttpRequest'
  PATH_INFO: '/api/genomes/PF3D7'
  QUERY_STRING: 'low=0&num=100'
  REMOTE_ADDR: '127.0.0.1'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '0.0.0.0'
  SERVER_PORT: '8081'
  SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0x6b37cd0>
  is_api_request: True
  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351'>, 'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x748eed0>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x795c310>
  paste.parsed_querystring: ([('low', '0'), ('num', '100')], 'low=0&num=100')
  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
  request_id: 'c1be491ec06811e39ed60025905a9e10'
  webob._parsed_query_vars: (MultiDict([('low', '0'), ('num', '100')]), 'low=0&num=100')
  wsgi process: 'Multithreaded'
------------------------------------------------------------

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