(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 aarthimohan11@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:
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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 jgoecks@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 aarthimohan11@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:
To search Galaxy mailing lists use the unified search at:
galaxy-dev@lists.galaxyproject.org
-
Aarthi Mohan -
Jeremy Goecks