Re: [galaxy-user] Sniffers not working

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