Il giorno mar, 19/02/2013 alle 20.38 +0000, Peter Cock ha scritto: > On Tue, Feb 19, 2013 at 6:45 PM, Nicola Soranzo <sora...@crs4.it> wrote: > > Il giorno mar, 19/02/2013 alle 14.15 +0000, Peter Cock ha scritto: > >> On Tue, Feb 19, 2013 at 2:00 PM, James Taylor <ja...@jamestaylor.org> > >> wrote: > >> > On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock wrote: > >> >>I think it could make sense to define generic 'asn1' and > >> >>'asn1-binary' formats in the Galaxy core (name suggestions > >> >>welcome) > > > > What about > > > > extension="asn" type="galaxy.datatypes.data:GenericAsn1" > > > > and > > > > extension="asnb" type="galaxy.datatypes.binary:GenericAsn1Binary" > > > > like GenericXml class? > > Those seem sensible to me as the class names, although I'm > not so sure about the format names (aka 'extensions' in Galaxy > terms). I'd prefer to see the '1' in the name for clarity. My > suggestions of 'asn1' and 'asn1-binary' were based on NCBI usage.
Ok, no problem! > >> Nicola - do you want to make a pull request to galaxy-central defining > >> ASN.1 text and binary formats (which we can then subclass for the > >> NCBI BLAST+ wrappers)? Or should I? > > > > If you mean a minimal implementation, I can surely do that. If something > > more elaborated is needed, then probably you are more qualified than me! > > The current minimal implementation you sent me for BLAST+ > would be an excellent start. Things like data type sniffers etc > would be a nice to have feature, but can be added later I think. > And the sooner this gets into the Galaxy core, the sooner we > can use it in the BLAST+ wrappers :) Before proceeding on this route, one question: we are going to introduce a dependency for blast_datatypes/ncbi_blast_plus on a future galaxy release, is it ok? I don't think it is possible to express such dependency in a repository_dependencies.xml file yet. Best, Nicola -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ ___________________________________________________________ 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/