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
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> Biomolecular Mass Spectrometry & Proteomics group
> Utrecht University
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> email: pieter.neerincx(a)gmail.com
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