Hi Nate, Thanks for the fast reply and fix! I'll give the update a try... Cheers, Pi On Aug 18, 2010, at 9:16 PM, Nate Coraor wrote:
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@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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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