June 2013 - galaxy-dev - lists.galaxyproject.org

Problem installing tools on cloud instance
by Brad Zeitner 26 Jun '13

26 Jun '13

I've started up an instance using cloudman, and it seemed to be running fine. When I tried to install a tool from the toolshed I got an error, and in trying to resolve the error I used the admin console to update galaxy. Now when Galaxy tries to start I get the following error: galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'sam_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'twobit' galaxy.tools.data DEBUG 2013-06-26 22:20:49,999 Loaded tool data table 'lift_over' Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 95, in __init__ from_shed_config=False ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 56, in load_from_config_file tree = util.parse_xml( config_filename ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py", line 132, in parse_xml tree = ElementTree.parse(fname) File "/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './shed_tool_data_table_conf.xml' Removing PID file paster.pid How do I resolve the no such file or directory error? I found an email conversation on this that said to restart galaxy, and I've done this multiple times but the problem is persisting. Thanks, -Brad

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DRMAA Runner URL Specify TORQUE host
by Bart Gottschalk 26 Jun '13

26 Jun '13

Is it possible to specify the torque host as part of a DRMAA runner URL? I haven't been able to find a *native_options *parameter to allow for this. I'm using the old style cluster configuration. *drmaa://[native_options]/* * * Also, I haven't been able to find a list of native_options anywhere. Does anyone have a link to a comprehensive list? - Bart

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Styling the Galaxy tool config xml
by graham etherington (TSL) 26 Jun '13

26 Jun '13

Hi, I'm trying to see if I can style Galaxy tools, so instead of all the input fields being a long list one after the other, I can align a few of the fields side-by-side. Has anyone any suggestions on how I might accomplish this? Best wishes, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601

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Fwd: How to Clean up Old Data
by greg 26 Jun '13

26 Jun '13

(I'm resending this, it didn't seem to go through) ---------- Forwarded message ---------- From: greg <margeemail(a)gmail.com> Date: Thu, Jun 13, 2013 at 9:29 AM Subject: Re: [galaxy-dev] How to Clean up Old Data To: Björn Grüning <bjoern.gruening(a)pharmazie.uni-freiburg.de> Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Hi Bjorn, Could I have a look at your cron job for this? I'm not completely sure what to schedule. Thanks, Greg On Mon, Mar 11, 2013 at 1:17 PM, greg <margeemail(a)gmail.com> wrote: > Thanks. Could I have a look at what your cron job looks like? > > -Greg > > On Mon, Mar 11, 2013 at 11:58 AM, Björn Grüning > <bjoern.gruening(a)pharmazie.uni-freiburg.de> wrote: >> Hi Greg, >> >>> I'm trying to figure out how to reduce the data stored on the galaxy server. >>> >>> I came across this page and it looks like data will get deleted if the >>> history element gets deleted but I can't tell if this happens >>> automatically or if I need to cron these scripts: >>> http://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20… >>> >>> Is there anything else I can do to clean up unused data? >> >> No that should be sufficient. You need to run >> >> python cleanup_datasets.py universe_wsgi.ini -d 60 >> >> with the different parameters ... -1 -2 -3 .... >> It will not happen automatically, i recommend you to set up a cron job >> that runs every week. You also may want to change the -d 60 to something >> less than 60. >> >>> Also is there a way a user can keep her history around as a record of >>> what was done and be able to rerun it later, but still delete the >>> actual data? >> >> I don't think that is possible at the moment. >> Cheers, >> Bjoern >> >>> Thanks, >>> >>> Greg >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >>

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Bowtie2 Specifying -k value (Alignment Search)
by Adam Brenner 26 Jun '13

26 Jun '13

One of our users has requested to see if we could add specifying an alignment search option to Bowtie2 (-k and -a option http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#default-mode-search-… ) Is this something anyone else has added to their galaxy installs? If so, how? I was looking at galaxy/dist/tools/sr_mapping/bowtie2_wrapper.* and it does not seem to challenging to add another field where a user could specify some integer value that we simply pass to the the <command> tag in the xml file. Would this be the correct way to go about this? Thanks in advanced! -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

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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 25 Jun '13

25 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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