May 2011 - galaxy-dev - lists.galaxyproject.org

restarting galaxy while tools/jobs are running
by Shantanu Pavgi 19 May '11

19 May '11

If we restart galaxy server then would it disturb galaxy-tools jobs that are running? e.g. I want to restart galaxy server while a user is running bowtie job/process. Will galaxy lose any context of this job/process after restart? -- Thanks, Shantanu.

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[Galaxy #13918] Fwd: [Galaxy #14246] Select first/last N rows from grouped tabular files (e.g. top BLAST hits)
by madduri 19 May '11

19 May '11

I wonder if somebody can give me more context around this issue.. Begin forwarded message: > From: "Peter Cock" <galaxy(a)ci.uchicago.edu> > Date: May 17, 2011 12:33:17 PM EDT > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] [Galaxy #14246] Select first/last N rows from grouped tabular files (e.g. top BLAST hits) > Reply-To: galaxy(a)ci.uchicago.edu > > On Tue, May 17, 2011 at 5:30 PM, Galaxy Support Tickets > <galaxy(a)ci.uchicago.edu> wrote: >> Dear Galaxy@iBi user: >> >> This message has been automatically generated in response to the creation of >> a Galaxy@iBi request regarding: >> >> "Select first/last N rows from grouped tabular files (e.g. top BLAST hits)" >> >> Your ticket has been assigned an ID of [Galaxy #14246]. >> >> >> Please include the string: >> >> [Galaxy #14246] >> > > This continues a discussion started under your reference [Galaxy > #13918], assigned to Alex Rodriguez. > > Peter > > ___________________________________________________________ > 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/ -- Ravi K Madduri The Globus Alliance | Argonne National Laboratory | University of Chicago http://www.mcs.anl.gov/~madduri

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Re: [galaxy-dev] wait thread: <1002:Not enough memory.> error > after enabling DRMAA
by Mariusz Mamoński 19 May '11

19 May '11

Hi, > ------------------------------ > > Message: 13 > Date: Wed, 18 May 2011 17:15:06 +0200 > From: Leandro Hermida <softdev(a)leandrohermida.com> > To: Galaxy Dev <galaxy-dev(a)bx.psu.edu> > Subject: [galaxy-dev] wait thread: <1002:Not enough memory.> error > after enabling DRMAA > Message-ID: <BANLkTi=J4-ct04U=8dm6ra=sJcR_eDEG1A(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > I enabled DRMAA on my test Galaxy server installation and in the server > startup output I get the following strange "E #14ca [ 1.10] * wait are you using LSF? > thread: <1002:Not enough memory.>" lines after loading the job manager: > > ... > galaxy.jobs.runners.local INFO 2011-05-18 17:10:23,025 starting workers > galaxy.jobs.runners.local DEBUG 2011-05-18 17:10:23,026 5 workers ready > galaxy.jobs DEBUG 2011-05-18 17:10:23,026 Loaded job runner: > galaxy.jobs.runners.local:LocalJobRunner > galaxy.jobs.runners.drmaa DEBUG 2011-05-18 17:10:23,130 3 workers ready > galaxy.jobs DEBUG 2011-05-18 17:10:23,130 Loaded job runner: > galaxy.jobs.runners.drmaa:DRMAAJobRunner > galaxy.jobs INFO 2011-05-18 17:10:23,131 job manager started > E #14ca [ 0.00] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.02] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.05] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.07] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.10] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.12] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.15] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.17] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.20] * wait thread: <1002:Not enough memory.> > galaxy.jobs INFO 2011-05-18 17:10:23,373 job stopper started > E #14ca [ 0.22] * wait thread: <1002:Not enough memory.> > galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,383 > Loaded external_service_type: Simple unknown sequencer 1.0.0 > galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,386 > Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,400 Enabling 'admin' > controller, class: AdminGalaxy > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,402 Enabling 'async' > controller, class: ASync > E #14ca [ 0.25] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.27] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,428 Enabling 'dataset' > controller, class: DatasetInterface > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,432 Enabling 'error' > controller, class: Error > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,436 Enabling > 'external_service' controller, class: ExternalService > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,437 Enabling > 'external_services' controller, class: ExternalServiceController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,439 Enabling 'forms' > controller, class: Forms > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,441 Enabling 'history' > controller, class: HistoryController > E #14ca [ 0.30] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,460 Enabling 'library' > controller, class: Library > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,461 Enabling > 'library_admin' controller, class: LibraryAdmin > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,462 Enabling > 'library_common' controller, class: LibraryCommon > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,475 Enabling 'mobile' > controller, class: Mobile > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,478 Enabling 'page' > controller, class: PageController > E #14ca [ 0.32] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,482 Enabling > 'request_type' controller, class: RequestType > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,483 Enabling 'requests' > controller, class: Requests > E #14ca [ 0.35] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,508 Enabling > 'requests_admin' controller, class: RequestsAdmin > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,509 Enabling > 'requests_common' controller, class: RequestsCommon > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,511 Enabling 'root' > controller, class: RootController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,514 Enabling 'tag' > controller, class: TagsController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,519 Enabling > 'tool_runner' controller, class: ToolRunner > E #14ca [ 0.37] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.40] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,558 Enabling 'tracks' > controller, class: TracksController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,562 Enabling > 'ucsc_proxy' controller, class: UCSCProxy > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,564 Enabling 'user' > controller, class: User > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,567 Enabling > 'visualization' controller, class: VisualizationController > E #14ca [ 0.42] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.45] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.47] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.50] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.53] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.55] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.58] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,747 Enabling 'workflow' > controller, class: WorkflowController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,755 Enabling 'contents' > API controller, class: ContentsController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,757 Enabling 'forms' API > controller, class: FormDefinitionAPIController > E #14ca [ 0.60] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,762 Enabling 'libraries' > API controller, class: LibrariesController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,767 Enabling > 'request_types' API controller, class: RequestTypeAPIController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,768 Enabling 'requests' > API controller, class: RequestsAPIController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,770 Enabling 'roles' API > controller, class: RoleAPIController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,772 Enabling 'samples' > API controller, class: SamplesAPIController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,773 Enabling 'users' API > controller, class: UserAPIController > E #14ca [ 0.63] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.65] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.67] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.70] * wait thread: <1002:Not enough memory.> > galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,862 Enabling 'httpexceptions' > middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,869 Enabling 'remote user' > middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,871 Enabling 'recursive' > middleware > E #14ca [ 0.72] * wait thread: <1002:Not enough memory.> > galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,882 Enabling 'print debug' > middleware > E #14ca [ 0.74] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.77] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.79] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.82] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.85] * wait thread: <1002:Not enough memory.> > /gpfshpc/home/lhermida/soft/galaxy/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/exceptions/serial_number_generator.py:11: > DeprecationWarning: the md5 module is deprecated; use hashlib instead > import md5 > E #14ca [ 0.87] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.90] * wait thread: <1002:Not enough memory.> > galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,058 Enabling 'eval exceptions' > middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,062 Enabling 'trans logger' > middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,062 Enabling 'config' > middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,064 Enabling > 'x-forwarded-host' middleware > Starting server in PID 5229. > serving on http://10.155.10.23:8082 > E #14ca [ 0.92] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.95] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.97] * wait thread: <1002:Not enough memory.> > ... > > Do I need to increase some kind of running memory somewhere or is it another > problem? i think it is a bug. Could you try to edit the LSF_TOP/conf/lsf_drmaa.conf and set there wait_thread: 0 ? Unfortunately i do not have access to any LSF cluster so i can not dig further into this problem. > > thanks, > Leandro >

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Re: [galaxy-dev] issue with LSB_DEFAULTQUEUE
by Marina Gourtovaia 19 May '11

19 May '11

Hi Leandro I do not think the binding is env var aware. I used the following string in Galaxy drmaa configuration in universe_wsgi.ini default_cluster_job_runner = drmaa://-q srpipeline -P pipeline/ -q for the queue and -P for the project Marina On 19/05/2011 12:54, Leandro Hermida wrote: > Hi Marina, > > Thank you so much for your help, LSF DRMAA is working fine with Galaxy > now. > > One final problem though... if I specify the env var LSB_DEFAULTQUEUE > to a specific queue the Galaxy server appears in the log to submit the > job but it doesn't ever seem to get executed and looking in LSF with > bjobs -u all we don't see any galaxy submitted jobs, strange. Is > there something I am not setting up right with the particular queue? > > best, > Leandro > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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BioMart -> Galaxy returns html
by Liisa Koski 18 May '11

18 May '11

Hi, I'm trying to grab data from my local custom BioMart and export it to my local Galaxy installation. I did this by changing the address in the biomart.xml file <inputs action="http://mydomain/biomart/martview" check_values="false" method="get" target="_top"> <display>go to BioMart Central $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> </inputs> The file it returns is html. When I change the data type to tabular and click on the eye I see the following... <HTML> <BODY><CENTER> <font color="red"><big>Request Error (invalid_request)</big></font> <BR><BR> <big>Your request could not be processed. Request could not be handled</big> <BR><BR> <form action="http://domain.com/scripts/proxy_exception_2.pl" method="post"> <input type=hidden name=User value=""> <input type=hidden name=ClientIP value="ip.address.here"> <input type=hidden name=ProxyIP value="ip.address.here"> <input type=hidden name=URLHost value=""> <input type=hidden name=Exception value="Request Error-:-invalid_request-:-"> <input type=hidden name=DateTime value="2011-05-18-:-18:15:58"> <input type=submit name=mysubmit value="Request"> assistance from the internet support group. </form> </BODY> </HTML> Any help would be much appreciated. Thanks, Liisa

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wait thread: <1002:Not enough memory.> error after enabling DRMAA
by Leandro Hermida 18 May '11

18 May '11

Hi all, I enabled DRMAA on my test Galaxy server installation and in the server startup output I get the following strange "E #14ca [ 1.10] * wait thread: <1002:Not enough memory.>" lines after loading the job manager: ... galaxy.jobs.runners.local INFO 2011-05-18 17:10:23,025 starting workers galaxy.jobs.runners.local DEBUG 2011-05-18 17:10:23,026 5 workers ready galaxy.jobs DEBUG 2011-05-18 17:10:23,026 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.runners.drmaa DEBUG 2011-05-18 17:10:23,130 3 workers ready galaxy.jobs DEBUG 2011-05-18 17:10:23,130 Loaded job runner: galaxy.jobs.runners.drmaa:DRMAAJobRunner galaxy.jobs INFO 2011-05-18 17:10:23,131 job manager started E #14ca [ 0.00] * wait thread: <1002:Not enough memory.> E #14ca [ 0.02] * wait thread: <1002:Not enough memory.> E #14ca [ 0.05] * wait thread: <1002:Not enough memory.> E #14ca [ 0.07] * wait thread: <1002:Not enough memory.> E #14ca [ 0.10] * wait thread: <1002:Not enough memory.> E #14ca [ 0.12] * wait thread: <1002:Not enough memory.> E #14ca [ 0.15] * wait thread: <1002:Not enough memory.> E #14ca [ 0.17] * wait thread: <1002:Not enough memory.> E #14ca [ 0.20] * wait thread: <1002:Not enough memory.> galaxy.jobs INFO 2011-05-18 17:10:23,373 job stopper started E #14ca [ 0.22] * wait thread: <1002:Not enough memory.> galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,383 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,386 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,400 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,402 Enabling 'async' controller, class: ASync E #14ca [ 0.25] * wait thread: <1002:Not enough memory.> E #14ca [ 0.27] * wait thread: <1002:Not enough memory.> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,428 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,432 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,436 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,437 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,439 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,441 Enabling 'history' controller, class: HistoryController E #14ca [ 0.30] * wait thread: <1002:Not enough memory.> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,460 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,461 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,462 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,475 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,478 Enabling 'page' controller, class: PageController E #14ca [ 0.32] * wait thread: <1002:Not enough memory.> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,482 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,483 Enabling 'requests' controller, class: Requests E #14ca [ 0.35] * wait thread: <1002:Not enough memory.> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,508 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,509 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,511 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,514 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,519 Enabling 'tool_runner' controller, class: ToolRunner E #14ca [ 0.37] * wait thread: <1002:Not enough memory.> E #14ca [ 0.40] * wait thread: <1002:Not enough memory.> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,558 Enabling 'tracks' controller, class: TracksController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,562 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,564 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,567 Enabling 'visualization' controller, class: VisualizationController E #14ca [ 0.42] * wait thread: <1002:Not enough memory.> E #14ca [ 0.45] * wait thread: <1002:Not enough memory.> E #14ca [ 0.47] * wait thread: <1002:Not enough memory.> E #14ca [ 0.50] * wait thread: <1002:Not enough memory.> E #14ca [ 0.53] * wait thread: <1002:Not enough memory.> E #14ca [ 0.55] * wait thread: <1002:Not enough memory.> E #14ca [ 0.58] * wait thread: <1002:Not enough memory.> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,747 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,755 Enabling 'contents' API controller, class: ContentsController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,757 Enabling 'forms' API controller, class: FormDefinitionAPIController E #14ca [ 0.60] * wait thread: <1002:Not enough memory.> galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,762 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,767 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,768 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,770 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,772 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,773 Enabling 'users' API controller, class: UserAPIController E #14ca [ 0.63] * wait thread: <1002:Not enough memory.> E #14ca [ 0.65] * wait thread: <1002:Not enough memory.> E #14ca [ 0.67] * wait thread: <1002:Not enough memory.> E #14ca [ 0.70] * wait thread: <1002:Not enough memory.> galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,862 Enabling 'httpexceptions' middleware galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,869 Enabling 'remote user' middleware galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,871 Enabling 'recursive' middleware E #14ca [ 0.72] * wait thread: <1002:Not enough memory.> galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,882 Enabling 'print debug' middleware E #14ca [ 0.74] * wait thread: <1002:Not enough memory.> E #14ca [ 0.77] * wait thread: <1002:Not enough memory.> E #14ca [ 0.79] * wait thread: <1002:Not enough memory.> E #14ca [ 0.82] * wait thread: <1002:Not enough memory.> E #14ca [ 0.85] * wait thread: <1002:Not enough memory.> /gpfshpc/home/lhermida/soft/galaxy/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/exceptions/serial_number_generator.py:11: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 E #14ca [ 0.87] * wait thread: <1002:Not enough memory.> E #14ca [ 0.90] * wait thread: <1002:Not enough memory.> galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,058 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,062 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,062 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,064 Enabling 'x-forwarded-host' middleware Starting server in PID 5229. serving on http://10.155.10.23:8082 E #14ca [ 0.92] * wait thread: <1002:Not enough memory.> E #14ca [ 0.95] * wait thread: <1002:Not enough memory.> E #14ca [ 0.97] * wait thread: <1002:Not enough memory.> ... Do I need to increase some kind of running memory somewhere or is it another problem? thanks, Leandro

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Increase select multiple menu width for <param> tag type="data"
by Leandro Hermida 18 May '11

18 May '11

Hi, Is there a way to increase the width of a select multiple menu for a <param> tag type="data"? Certain dataset labels I have are very informative :) (i.e. long) and when used as an input to a tool you can't read what the difference is between each item unless you look at the dataset number and look back at the history. regards, Leandro

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Published Workflows menu location
by Peter Cock 18 May '11

18 May '11

Hi all, I recently started trying out the "Share workflow" functionality on our local Galaxy, so that I could make available some general interest workflows to all our users, rather than sharing them with individuals one by one. However, once published, it was not easy to find them! I eventually found them under the "Shared Data" drop down menu entry "Published Workflows" (yet "Shared" workflows are not on this menu). The captions "Shared" and "Published" seem to be used inconsistently. Maybe the top level "Shared Data" menu should be renamed to "Shared Resources" or "Published Resources"? To me, workflows are not data, and so should not be under "Shared Data". Rather, I expected them to be under the "Workflow" menu. Is the separation because in order to run or edit a "Published Workflows", you must first import it? Perhaps a simple solution would be a note and link at the bottom of the main "Workflow" page directing people to the "Published Workflows" page under the "Shared Data" drop down menu. Peter

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Select first/last N rows from grouped tabular files (e.g. top BLAST hits)
by Peter Cock 18 May '11

18 May '11

Hi all, I'm wondering if the following task can be done in Galaxy with the standard tools. The specific example is selecting the top (e.g. 3) match sequences for each blast query, but I see this problem as much more general than a "Select top BLAST hits" tool. I want to select the first few (e.g. 1) rows of each group in a tabular file, where the group criteria is having certain columns equal (e.g. the first 2). e.g. Tabular BLAST output has columns of query ID, match ID, etc. queryA match1 ... queryA match2 ... queryA match2 ... queryA match3 ... queryA match4 ... queryA match4 ... queryA match4 ... queryB match5 ... queryB match5 ... queryC match6 ... queryC match7 ... In this example, some of my queries have more than one HSP per match (more than one line with the same first two columns). If I group on the first two columns, the groups are: ------------------------ queryA match1 ... ------------------------ queryA match2 ... queryA match2 ... ------------------------ queryA match3 ... ------------------------ queryA match4 ... queryA match4 ... queryA match4 ... ------------------------ queryB match5 ... queryB match5 ... ------------------------ queryC match6 ... ------------------------ queryC match7 ... ------------------------ If I then take the first row in each group, that gives me just the first HSP for each query+match combination. queryA match1 ... queryA match2 ... queryA match3 ... queryA match4 ... queryB match5 ... queryC match6 ... queryC match7 ... If for example I wanted only the top 3 matches for each query, I could repeat the proposed tool one more time but with different settings - this time grouping on the first column only: queryA match1 ... queryA match2 ... queryA match3 ... queryB match5 ... queryC match6 ... queryC match7 ... I hope I've conveyed the idea here. The existing tools "Select first lines from a dataset" and "Select last lines from a dataset" are related, but do this at the file level. Does this make sense? Does it seem like a useful tool to write if there isn't anything like this already present? Or might it be simpler to just write a "Select top BLAST hits" tool? Peter

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Reciprocal Best Hits (RBH) from BLAST tabular output
by Peter Cock 18 May '11

18 May '11

Hi all, I mentioned just over a month ago that I had written a Galaxy tool to do find Reciprocal Best Hits (RBH) from BLAST tabular output or similar (e.g. Bill Pearson's FASTA tabular output). http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004825.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004829.html The only problem I had was setting default columns, which I consider to be a minor bug in Galaxy: https://bitbucket.org/galaxy/galaxy-central/issue/507 Regardless of this small usability issue, would the Galaxy team like to add this tool to the main distribution (to sit along with my BLAST+ wrappers), or should I submit it to the tool shed? If you want to merge it, the following change set should suffice: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 I made a subsequent change set to test giving column defaults as value="c2" rather than value="c2" which makes no difference, but if this is how default column values are meant to be given, take this change too: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 Thanks, Peter

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