-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Björn,
On 07/16/2014 09:20 AM, Björn Grüning wrote: > 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. Okay, good, as I figured then. >> 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 Those absolutely should be, thank you. I'll probably strip them down and post a minimal working example, and code to the wiki as well, for future reference. > 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? Ja, sounds good! Happy to help. > > 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: >>>> > 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 >>>>> ___________________________________________________________ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> http://lists.bx.psu.edu/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> http://lists.bx.psu.edu/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >> - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (GNU/Linux) iQIcBAEBAgAGBQJTxo7pAAoJEMqDXdrsMcpVKnsP/3Oqaux9jdJobAuCL4py5wW9 Kbxe5Io5ua8ZhrDUj4qeQsYzNPt9bHKuYWK1VHz+Jf8ZPZDW6a/hHTf6mTqfXrzX mDUHtf9j6xEW+ye1JTL7QsOImxl7JRDvI0MVQOkQt8C8QZTWu+pjXLMrVd/QygGL AntX/1ngmEYDKxwPAagD+P1bUxwNalZ96FE9qIubL5GLjFn7yuG6fBE98/40UM27 x4bHdRB+svUTjCiH/E7MKZGN2OEL8H6QHOnl7rfA70Z2SezNr7Ivzgb+pVStyVum QF2/g8C0dUooYaM2hZhosOM6mLKSNH2NAIsRumfIQMDoZBMxlQE6iD0550tORvSf 1MP1T2B0jqPckca30udDZ7qtksB0u/QJgLFunZ26uQZE/B/jKoL/FjNsNIFgxCto EdIab40rH7ysnFjbiLV8AiSjgDV0V8VCDjxNbBZRjwy34RP2ZN4Ggew+vyGVv3iH 28biFIhbxVWmYccDYGWVYaqw2wdUdk4l9j0OvlCaqHH3fXsPyhpAWivmVzwc3kGz /Wyj3KYMEySiJ++Wkw1H29QH0wyEpbh89dX2ULQjqJV7qibWUM7KZtFiizEr55tP QI0KhJzGe/NQ4CzP1szl/mbxjBUr3cRGXF1dausVu1hKgjhb2QJBJKw9nFvbTnKw BKOkNRQ/vkr3aHL1IrVE =AP7s -----END PGP SIGNATURE----- ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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