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
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