Re: [galaxy-dev] Where are the datatype associations stored?
Yeah, I had messed around with the database already, but removing the repository worked...Not sure why it was still loading it, but its all cool now...Thanks!ThonOn Jul 11, 2012, at 04:20 PM, Greg Von Kuster wrote:How did you try to remove the tool? Do you mean that you used the Galaxy Admin UI to Uninstall the repository? The datatypes are defined in a file named datatypes_conf.xml in the installed gmap repository. Assuming you can uninstall this repository, doing so will eliminate this problem. I do not recommend nuking tables. If you manually deleted rows from your database tables, you may have caused problems with your environment that could render it un-useable.On Jul 11, 2012, at 6:46 PM, Anthonius deBoer wrote:Hi,I had some more bad luck trying to install the GMAP stuff from the TOOLSHEd but revision 10 is broken since it does not allow you to select a section and just stores the programs in the main tree...But when I tried to remove the tool I got the following error for every run, since the sniffers where still looking for a module called GMAP...Which table should I nuke to get rid of this association? Where are the datatype associations stored?There does not seem to be an XML file for this, so I hope i can just remove some lines from the postgres database table but there are no obvious table names I can find...WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntervalAnnotation' to sniff_order: No module named g! map WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SpliceSiteAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntronAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SNPAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntervalAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SpliceSiteAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntronAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SNPAnnotation' to sniff_order: No module named gmapThanks ___Please keep all replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ 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] Where are the datatype associations stored?
How did you try to remove the tool? Do you mean that you used the Galaxy Admin UI to Uninstall the repository? The datatypes are defined in a file named datatypes_conf.xml in the installed gmap repository. Assuming you can uninstall this repository, doing so will eliminate this problem. I do not recommend nuking tables. If you manually deleted rows from your database tables, you may have caused problems with your environment that could render it un-useable. On Jul 11, 2012, at 6:46 PM, Anthonius deBoer wrote: > Hi, > > I had some more bad luck trying to install the GMAP stuff from the TOOLSHEd > but revision 10 is broken since it does not allow you to select a section and > just stores the programs in the main tree... > > But when I tried to remove the tool I got the following error for every run, > since the sniffers where still looking for a module called GMAP... > > Which table should I nuke to get rid of this association? Where are the > datatype associations stored? > There does not seem to be an XML file for this, so I hope i can just remove > some lines from the postgres database table but there are no obvious table > names I can find... > > WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype > 'galaxy.datatypes.gmap:IntervalAnnotation' to sniff_order: No module named g! > map > WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype > 'galaxy.datatypes.gmap:SpliceSiteAnnotation' to sniff_order: No module named > gmap > WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype > 'galaxy.datatypes.gmap:IntronAnnotation' to sniff_order: No module named gmap > WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype > 'galaxy.datatypes.gmap:SNPAnnotation' to sniff_order: No module named gmap > WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype > 'galaxy.datatypes.gmap:IntervalAnnotation' to sniff_order: No module named > gmap > WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype > 'galaxy.datatypes.gmap:SpliceSiteAnnotation' to sniff_order: No module named > gmap > WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype > 'galaxy.datatypes.gmap:IntronAnnotation' to sniff_order: No module named gmap > WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype > 'galaxy.datatypes.gmap:SNPAnnotation' to sniff_order: No module named gmap > > Thanks > ___ > 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/ ___ 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/
