Is this going to work? I get that this would be a better design if done from the beginning, but what happens if you install an emboss repository upgrade (on an existing install) that brings in conflicting types from other repositories that already exist and have been previously installed? Does the tool shed have a mechanism to handle that?
-John On Wed, Jul 16, 2014 at 9:20 AM, Björn Grüning <bjoern.gruen...@gmail.com> 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. > > >> 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: >>>> >>>>> -----BEGIN PGP SIGNED MESSAGE----- >>>>> Hash: SHA1 >>>>> >>>>> 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 >>>>> -----BEGIN PGP SIGNATURE----- >>>>> Version: GnuPG v2.0.22 (GNU/Linux) >>>>> >>>>> iQIcBAEBAgAGBQJTxCHwAAoJEMqDXdrsMcpVmbsQAJ3eFIhZtZmVP9LCz/F9Ywg/ >>>>> 148NJZy4lmxZU0KScJlc8kVDCDSADXIHd0Db/kpJwuUKEX7zei9q2uXfO7sWl3yt >>>>> yxrFEdtX/a5SMVsa6F5WZuKwBs0zfvfsnIUoraOgh6nXeJnr53l9mYeWaKB6bi3Z >>>>> xAlgJG/kdIR1jRjAimuQf4vMjNgtDQPOmotYBQTytbhsV6/nRzGI8RZAYwQ7GnVs >>>>> XYOWFyhzrBgALndVI3BjI21rbRqguhrqr2t7i0Ma7Pp2JmAnNjmUaq70NN3Rueh6 >>>>> DvnTtxInM1dVOQY+Yam6MCMmAedV1cG+rNGdpP2l82MajQAsMtbXckBXXKcSgyTq >>>>> WCFoLVURYO1tHkWyq4ikamfFDHtJp1DogBYhUiPMyRw+CV+3sOvr0U5DcyRdiDsJ >>>>> Xcm3ygqYVLGwauNmuN3yGcQcnfypDOOeFs1lppbNe3lw0w3ikZN4Zmu1ec5s1ITK >>>>> MEcgBrGYgZrKDRXkx53lnABGpv6mYflYpag7fguDNL8j0lh9beaaNmHr4tmeEcug >>>>> VZ1b1EWoLMj/ikJ/vZcluiHPTSTheiAP8Ttvh1WAayq4rKwVtZygaI9IDauqqBQ1 >>>>> Dgotes3vcomlTQXDUEZACyOZDxl7wbAUh0LZVaa2fYNIOoPNPOItUFSjf6YveF88 >>>>> dLiw3ddVm+BFmczJzRpt >>>>> =4m2j >>>>> -----END PGP SIGNATURE----- >>>>> ___________________________________________________________ >>>>> >>>>> 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/ >> >> > ___________________________________________________________ > > 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/
