Hi Jeremy, Thanks for pointing it out. It was indeed an extra line at end of file that caused the problem. It works fine now.
I think for organism not found in UCSC, best solution is to upload the genome fasta file and go for edit attributes -> convert FASTA to 2bit and len file . Thanks RT On Thu, Apr 10, 2014 at 9:04 PM, Jeremy Goecks <jgoe...@gwu.edu> wrote: > (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' > ------------------------------------------------------------ > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > >
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