Hi Eric,
Forgive me, I'm not 100% clear on the custom plugin system used by galaxy, but if I
"subclass" from the text data type, will sniffers I implement override text's
and function? The lack of being able to add an entry to the sniffer section (unlike with
the tabular example) led me to believe my genbank datatype wouldn't be sniffed.
Thats true, if you want to override functions, you need to subclass it
on a python level not on the XML level.
Additionally, I'd still like to be able to add completely new datatypes, do you
know of any working examples of this? As mentioned in my original post,
duplicating an existing datatype and changing names on it surprisingly doesn't
work.
https://github.com/bgruening/galaxytools/tree/master/datatypes/msa_datatypes
https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatypes/datatypes_conf.xml
Is that enough, to get started?
I'd be lovely to have the emboss datatypes split out.
Ok, than lets start :)
I will try to fork emboss into my galaxytools/datatypes repository and
try to split them. You will get commit access and can improve your
genbank datatype (and a few more ;)). Finally, we will talk to the
devteam to rewrite EMBOSS to depend on our separate data type
repositories. OK?
Ciao,
Bjoenr
Cheers,
Eric
On July 16, 2014 8:34:55 AM CDT, Peter Cock <p.j.a.c...@googlemail.com> wrote:
Indeed - ideally (once working) we can upload under the IUC ToolShed as
a
community maintained resource rather than under a personal account
which
becomes a single point of failure (the bus factor).
We (the ICU) have previously discussed doing this so that the EMBOSS
datatypes could become more of a meta-entry depending on other smaller
specific datatype defining ToolShed repositories. But it hasn't reached
the
top of my personal TODO list yet ;)
Peter
On Wed, Jul 16, 2014 at 1:47 PM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:
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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