- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] How to enable auto option for newly added file formats
by Peter Cock 26 Jun '13

26 Jun '13

On Tue, Jun 25, 2013 at 8:28 AM, shashi shekhar <me_shashi29(a)yahoo.co.in> wrote: > Hi, > > yeah ..it is same thing... but i followed the galaxy -datatype(how to add > new file format)tutorial ..but still my newly added file format is not > working with auto option ....it always display txt format ..it is similar to > txt format with some specific property .. > > Reagrds > shashi So you've followed this: http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Have you tested your sniff method works? Have you checked the order the file types are tested? Peter P.S. Don't forget to CC the mailing list.

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unable to enter the Admin pages
by Berner, Thomas 26 Jun '13

26 Jun '13

Hi guys, we are currently establishing our own local Galaxy instance. However, after we tried to install the "mothur toolsuite" we could not enter the admin pages anymore. Every time we try we we obtain the following error: "Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team." Here is what the paster.log says: 172.31.30.58 - - [26/Jun/2013:11:02:14 +0200] "GET /history/get_display_application_links HTTP/1.0" 200 - "http://galaxy.jki.bund.de/history" "Mozilla/5.0 (Windows NT 6.1; rv:21.0) Gecko/20100101 Firefox/21.0" 172.31.30.58 - - [26/Jun/2013:11:02:33 +0200] "GET /admin HTTP/1.0" 500 - "http://galaxy.jki.bund.de/" "Mozilla/5.0 (Windows NT 6.1; rv:21.0) Gecko/20100101 Firefox/21.0" Error - <class 'simplejson.decoder.JSONDecodeError'>: Expecting object: line 1 column 65534 (char 65534) URL: http://galaxy.jki.bund.de/admin File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy/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 '/opt/galaxy/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 '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/opt/galaxy/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', line 31 in index installing_repository_ids = get_ids_of_tool_shed_repositories_being_installed( trans, as_string=True ) File '/opt/galaxy/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', line 1080 in get_ids_of_tool_shed_repositories_being_installed trans.model.ToolShedRepository.status == loading_datatypes_status ) ): File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2348 in instances File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2120 in _instance File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1974 in populate_state File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 150 in fetch_col File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py', line 658 in process File '/opt/galaxy/galaxy-dist/lib/galaxy/model/custom_types.py', line 52 in process_result_value return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) File '/opt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 402 in decode File '/opt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 418 in raw_decode JSONDecodeError: Expecting object: line 1 column 65534 (char 65534) CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3' HTTP_CACHE_CONTROL: 'max-age=0' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a29d379ce3a444c9b5d260e535a8d6224324fc4d09af0e63592f8cd6e92ad7996' HTTP_HOST: 'galaxy.jki.bund.de' HTTP_REFERER: 'http://galaxy.jki.bund.de/' HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; rv:21.0) Gecko/20100101 Firefox/21.0' HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)' HTTP_X_FORWARDED_FOR: '172.31.30.58' ORGINAL_REMOTE_ADDR: '172.16.20.52' PATH_INFO: '/admin' REMOTE_ADDR: '172.31.30.58' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.0' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x98fb190> is_api_request: False paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a29d379ce3a444c9b5d260e535a8d6224324fc4d09af0e63592f8cd6e92ad7996'>, 'galaxysession=c6ca0ddb55be603a29d379ce3a444c9b5d260e535a8d6224324fc4d09af0e63592f8cd6e92ad7996') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x9d5ad90> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xa33d990> 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: '2355c54cde3f11e294120050568d0b1f' webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------ Our system is: Linux version 2.6.32-5-amd64 (Debian 2.6.32-48squeeze1) (dannf(a)debian.org) (gcc version 4.3.5 (Debian 4.3.5-4) ) #1 SMP Mon Feb 25 00:26:11 UTC 2013 Thanks for any help. Regards, Thomas

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Toolshed bwa wrapper mistake
by Yec'han Laizet 26 Jun '13

26 Jun '13

Hello, I found two mistakes in the code of the bwa wrapper . The first one comes from the following error message: ----------- File "/galaxy-dist/tools/bwa_wrappers/bwa_wrapper.py", line 79 parser.add_option( '-y', '--ion', dest='ion', action="store_true, help='Ion Torrent data mode using bwasw' ) ^ SyntaxError: EOL while scanning string literal ----------- in the bwa_wrapper.py file line 79: -there is a missing double quote character after sur store_true in the bwasw_wrapper.xml file line 9: -there --ion option must not have a value Till, with those corrections, the mapping with bwa for Ion Torrent does not seem to work properly. My ouput sam file had only the header in it. Best regards Yec'han ================================================ Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _________________________________ Plateforme Genome Transcriptome INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ================================================

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GATK fasta file not found ERROR
by sridhar srinivasan 26 Jun '13

26 Jun '13

Dear Developers, I am using GATK for first time. I am doing Targeted reseq Analysis. while i am running Unified Genotyper in Galaxy interface. it gives error message as mentioned below.. "ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-WBrGTf) does not exist." But i places the Fasta file path in .loc file. Also could anyone tell what are the preprocessing steps before using Bam file for Unified Genotyper?? Your answers are very much Appericiated. Thanks Sridhar

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June update breaks saved histories
by Shane Sturrock 25 Jun '13

25 Jun '13

I've tried updating a couple of times to the latest stable release and each time I find that I can no longer see my saved histories. Roll back my machine to an earlier snapshot and it is fine. The thing that may be different about our system is that we're using Apache authentication rather than using the built in accounts. Nothing about the apache install has changed, just do the update to the June release, start it, run the manage_db.sh upgrade and restart (database is on postgres by the way) and then saved histories is empty and creating new histories never populates the list either. I would like to upgrade since the previous release had issues with sending BAM files to UCSC which this update has fixed. Maybe it's related to the upgraded SQLAlchemy? Shane -- For urgent cases, contact support(a)biomatters.com Dr Shane Sturrock shane.sturrock(a)biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand

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tool shed tools are not recognised in jobs_conf.xml
by Björn Grüning 25 Jun '13

25 Jun '13

Hi, I tried to increase the h_vmem setting for a tool shed tool in jobs_conf.xml, but nothing from the documented options [1] worked for me. However, it works for non tool shed tools. Did anyone see such a behaviour? We are using SGE/drmaa. Thanks, Björn [1] id="toolshed.example.org/repos/nate/filter_tool_repo/filter_tool/1.0.0" or id="toolshed.example.org/repos/nate/filter_tool_repo/filter_tool" or id="filter_tool"

1 0

Bowtie2 on a new local instance
by Mathew Moore 25 Jun '13

25 Jun '13

I installed a local instance of Galaxy, and (i believe) downloaded all of the dependencies, indexes, and modified the appropriate .loc files. Pretty much all of the tools work, except for Bowtie2. (I installed the bowtie tool, and it works perfectly) The bowtie2 sequence assembler completes with appropriate output from the command-line, but not from the WEB-GUI interface. When you run Bowtie2 from the web-GUI, it completes almost immediately, not with an error, but with a 62byte bam file. The output box in the gui indicates the file contents are 'binary bam alignments file'. For the record, I installed the bowtie2 example lamda indexes in Galaxy and modified the loc file. After running the example FQ files through the WEB-GUI I received the same 62Byte output, indicating it's not a file or index problem. Running this example on the command-line completes as expected. Has anyone seen this. I'm sure I did something stupid somewhere, I just can't seem to find it. Any assistance would be appreciated. Kind regards, Mat

1 0

galaxy cuffdiff running too long
by Robert Chase 25 Jun '13

25 Jun '13

Hello, When we run cuffdiff from the command line we get this; [galaxy@q ~]$ /bin/cuffdiff /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available (required by /bin/cuffdiff) cuffdiff v2.0.2 (3522) It looks like we are using a more recent version of cuffdiff than is supported by the galaxy tool wrappers (0.0.5 and 0.0.6). Using the 0.0.5 tool gives empty outputs. Using the 0.0.6 tool results in runs that last for five days without terminating. Has this behavior been seen before? How can we get good outputs to feed into cummeRbund? -Rob

3 5

BAM pileups bugging out
by Andrew Guo 25 Jun '13

25 Jun '13

After using tools to convert a SAM to a BAM file, I am trying to filter the BAM pileup. However, the filter BAM tool is not picking up on the dataset that I just created. It should show up under 10 column pileup, but an error message is saying "History does not include a dataset of the required format/build". Could you provide any insight into this? Thanks, Andrew

2 4

Error in using Trackster: datatypes_conf.xml
by Perez, Ricardo 25 Jun '13

25 Jun '13

Dear all, I am trying to set up trackster for my local instance in galaxy. I did the following: Uncommented from the universe_wsgi.ini; len_file_path = path/to/file/galaxy-dist/tool-data/shared/ucsc/chrom Also I ran the following commands: mkdir ./tool-data/shared/ucsc/chrom/ python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ However when I try to use trackster, I get the following message: "A converted for this file is not installed. Please heck your datatypes_conf.xml file." How exactly do I find out which converted files I am missing? I did the above steps in another instance of galaxy and Trackster works fine in there. Thank you for your time, --Ricardo Perez

2 1