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' ------------------------------------------------------------