On Jun 29, 2010, at 2:29 PM, Davide Cittaro wrote: > Hi all, > how does the library search tool work? I'm trying on the public galaxy but I can't get any result... > I mean, does it only work at "first level"? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */ _______________________________________________ galaxy-user mailing list galaxy-user(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

When I click the Options button in the tool pane on the left there's no option to search for tools. I can only show or hide recently used tools. Is there something I need to configure/enable to make this work? I browsed the Wiki, but could not find relevant documentation...

Hi all, I used to have working sniffers for custom data formats, but the documentation on the wiki is no longer enough to make it work :(... When I start our Galaxy I do see log messages like this: galaxy.datatypes.registry INFO 2010-08-17 18:20:28,666 Loaded sniffer for datatype: galaxy.datatypes.nbic:RAW which suggests that the sniffers should be enabled, but unfortunately they don't work. If I add the sniffers to the default list in galaxy/lib/galaxy/datatypes/registry.py like this: .... # Default values - the order in which we attempt to determine data types is critical # because some formats are much more flexibly defined than others. if len(self.sniff_order) < 1: self.sniff_order = [ nbic.RAW(), nbic.OtherCustomFormat(), binary.Bam(), binary.Sff(), xml.BlastXml(), sequence.Maf(), sequence.Lav(), sequence.csFasta(), etc..... my sniffers do work, so I'm pretty sure it's not the sniff-logic. Does anyone have an idea how I can make my sniffers work again by simply adding them to datatypes_conf.xml and importing them in registry.py, but without hacking the code in registry.py that builds the list of sniffers? Cheers, Pi ------------------------------------------------------------------ Biomolecular Mass Spectrometry & Proteomics group Utrecht University phone: +31 6 143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online visiting address: H.R. Kruyt building // room O607 Padualaan 8 // 3584 CH Utrecht // The Netherlands mail address: P.O. box 80.082 // 3508 TB Utrecht // The Netherlands ------------------------------------------------------------------ _______________________________________________ galaxy-user mailing list galaxy-user(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Hi Pieter, Thanks for reporting this. It should be fixed in changeset 4158:03be4a0828ce. Thanks, --nate Pieter Neerincx wrote: > Hi all, > I used to have working sniffers for custom data formats, but the documentation on the wiki is no longer enough to make it work :(... > When I start our Galaxy I do see log messages like this: > galaxy.datatypes.registry INFO 2010-08-17 18:20:28,666 Loaded sniffer for datatype: galaxy.datatypes.nbic:RAW > which suggests that the sniffers should be enabled, but unfortunately they don't work. If I add the sniffers to the default list in galaxy/lib/galaxy/datatypes/registry.py like this: > .... > # Default values - the order in which we attempt to determine data types is critical > # because some formats are much more flexibly defined than others. > if len(self.sniff_order) < 1: > self.sniff_order = [ > nbic.RAW(), > nbic.OtherCustomFormat(), > binary.Bam(), > binary.Sff(), > xml.BlastXml(), > sequence.Maf(), > sequence.Lav(), > sequence.csFasta(), > etc..... > my sniffers do work, so I'm pretty sure it's not the sniff-logic. Does anyone have an idea how I can make my sniffers work again by simply adding them to datatypes_conf.xml and importing them in registry.py, but without hacking the code in registry.py that builds the list of sniffers? > Cheers, > Pi > ------------------------------------------------------------------ > Biomolecular Mass Spectrometry & Proteomics group > Utrecht University > phone: +31 6 143 66 783 > email: pieter.neerincx(a)gmail.com > skype: pieter.online > visiting address: > H.R. Kruyt building // room O607 > Padualaan 8 // 3584 CH Utrecht // The Netherlands > mail address: > P.O. box 80.082 // 3508 TB Utrecht // The Netherlands > ------------------------------------------------------------------ > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user