[galaxy-dev] Published Workflows menu location
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 ___ 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/
Re: [galaxy-dev] Reciprocal Best Hits (RBH) from BLAST tabular output
On Wed, May 18, 2011 at 3:54 AM, Kanwei Li kan...@gmail.com wrote: Hi Peter, I think the tool shed would be appropriate for this... -K OK - I'll do that. Thanks, 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/
Re: [galaxy-dev] Select first/last N rows from grouped tabular files (e.g. top BLAST hits)
On Tue, May 17, 2011 at 5:30 PM, Peter Cock p.j.a.c...@googlemail.com wrote: 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. ... 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? While I still think the above task could be useful in general, I am now considering a general BLAST filter tool to offer this and some other commonly used filters like a minimum coverage threshold (which is possible with a filter on the extended tabular output, but not trivial). 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/
[galaxy-dev] wait thread: 1002:Not enough memory. error after enabling DRMAA
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] *
[galaxy-dev] Increase select multiple menu width for param tag type=data
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 ___ 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/
Re: [galaxy-dev] wait thread: 1002:Not enough memory. error after enabling DRMAA
Hi Leandro From our previous correspondence I remember that you are using LSF This is some sort of a bug in the latest drmaa-lsf binding. I moved to the previous version and everything is OK for me Marina On 18/05/2011 16:15, Leandro Hermida wrote: 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 http://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 http://galaxy.jobs DEBUG 2011-05-18 17:10:23,130 Loaded job runner: galaxy.jobs.runners.drmaa:DRMAAJobRunner galaxy.jobs http://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 http://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
Re: [galaxy-dev] wait thread: 1002:Not enough memory. error after enabling DRMAA
Hi Marina, Thanks... so are you using 1.0.3 instead of 1.0.4? best, leandro On Wed, May 18, 2011 at 6:56 PM, Marina Gourtovaia m...@sanger.ac.uk wrote: Hi Leandro From our previous correspondence I remember that you are using LSF This is some sort of a bug in the latest drmaa-lsf binding. I moved to the previous version and everything is OK for me Marina On 18/05/2011 16:15, Leandro Hermida wrote: 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
Re: [galaxy-dev] wait thread: 1002:Not enough memory. error after enabling DRMAA
Yes. M. On 18/05/2011 18:23, Leandro Hermida wrote: Hi Marina, Thanks... so are you using 1.0.3 instead of 1.0.4? best, leandro On Wed, May 18, 2011 at 6:56 PM, Marina Gourtovaia m...@sanger.ac.uk mailto:m...@sanger.ac.uk wrote: Hi Leandro From our previous correspondence I remember that you are using LSF This is some sort of a bug in the latest drmaa-lsf binding. I moved to the previous version and everything is OK for me Marina On 18/05/2011 16:15, Leandro Hermida wrote: 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 http://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 http://galaxy.jobs DEBUG 2011-05-18 17:10:23,130 Loaded job runner: galaxy.jobs.runners.drmaa:DRMAAJobRunner galaxy.jobs http://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 http://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
[galaxy-dev] BioMart - Galaxy returns html
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 displaygo 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 BODYCENTER font color=redbigRequest Error (invalid_request)/big/font BRBR bigYour request could not be processed. Request could not be handled/big BRBR 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___ 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/
