Hi Eric,

please have a look at:

https://github.com/bgruening/galaxytools/blob/master/datatypes/msa_datatypes/datatypes_conf.xml

You need somthing like:
<datatype extension="genbank" type="galaxy.datatypes.data:Text" subclass="True" />

Lets try to split the EMBOSS datatypes a little bit into small chunks. E.g. sequences_datatypes, msa_datatypes ... and so on ...

Cheers,
Bjoern


Am 14.07.2014 20:31, schrieb Eric Rasche:
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I'm trying to add a new datatype to my galaxy instance for genbank
files, however I'm running into various issues. I've followed the
tutorial (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)

however that example subclasses tabular, and I'd like to subclass Text
as they're plain text files, and I'd like to be able to define a sniffer
for them (not possible if your type=galaxy.datatypes.data:Text)

I figured the call ought to be something like

<datatype extension="gb" type="galaxy.datatypes.data:Genbank"
subclass="True" />

however, everything I try fails with

Error importing datatype module galaxy.datatypes.data: 'module' object has no 
attribute 'Genbank'

To avoid this particular issue, I tried writing a separate datatype just
for genbank files (type="galaxy.datatypes.genbank:Genbank"), however
that fails with the same error:

galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error importing 
datatype module galaxy.datatypes.genbank: 'module' object has no attribute 
'genbank'
Traceback (most recent call last):
   File "/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py", line 
206, in load_datatypes
     module = getattr( module, mod )
AttributeError: 'module' object has no attribute 'genbank'

Here's my lib/galaxy/datatypes/genbank.py looks like:

import pkg_resources
pkg_resources.require( "bx-python" )
import logging
from galaxy.datatypes import data
log = logging.getLogger(__name__)

class Genbank( data.Text ):
     file_ext = "gb"

     def sniff( self, filename ):
         header = open(filename).read(5)
         return header == 'LOCUS'

To debug this, I've tried copying the tabular data type completely,
removed all the classes other than Tabular, and renamed it "Genbank",
however this fails too with the same error.

Can anyone offer some insight?

Cheers,
Eric
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