(Moved to galaxy-dev mailing list because it concerns server admin rather than Galaxy usage.)If everything worked fine with a human build but not for PF3d7, then my guess is that the len file for PF3d7 isn’t correctly formatted. Right now, the file parser is very unforgiving—no extra spaces or lines are allowed.If you check the len file and don’t spot an issue, please send to it to me and I’ll take a look.Best,J.--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington UniversityOn Apr 10, 2014, at 2:30 AM, Aarthi Mohan <aarthimohan11@gmail.com> wrote:___________________________________________________________RTHi all,Thanks
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.
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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