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/
