(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 University



On Apr 10, 2014, at 2:30 AM, Aarthi Mohan <aarthimoha...@gmail.com> wrote:

> 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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