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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