[Bioc-devel] Moving from MakeOrganismPackage to AnnotationHub recipes

[Keith Hughitt]

Hello,

I have started putting together an AnnotationHub recipe for the TriTrypDB
<http://tritrypdb.org/tritrypdb/>. The goal is to write a generalized
recipe which can then be adopted for all of the other EuPathDB
<http://eupathdb.org/eupathdb/> databases.

I curently have code for generating OrgDb, TxDb, and OrganismDb packages
for any organism hosted on EuPathDB:

    https://github.com/elsayed-lab/eupathdb-organismdb

After reading the AnnotationHub and AnnotationHubData docs (e.g.
http://bioconductor.org/packages/release/bioc/vignettes/AnnotationHub/inst/doc/AnnotationHubRecipes.html),
I've started putting together an AnnotationHub recipe, following the
InParanoid example:


https://github.com/elsayed-lab/tritrypdb-annotation-hub-recipe/blob/master/tritrypdb_annotationhub_recipe.R

Generating the AnnotationHubMetaData objects seems pretty straight-forward
(although the Map function isn't behaving at the moment), however, it's a
little less clear how to go about creating the data side of the recipes.

Is it currently possible to host all three annotation dbs (Org, Tx, and
Organism) using AnnotationHub? If so, any suggestions for how to go about
it?

Since I can already generate the SQLite databases for each for each of the
packages, e.g. 1
<https://github.com/elsayed-lab/TxDb.TcruziCLBrenerEsmer.tritryp25.genes/tree/master/inst/extdata>,
2
<https://github.com/elsayed-lab/org.TcCLB.esmer.tritryp.db/tree/master/inst/extdata>,
3
<https://github.com/elsayed-lab/Trypanosoma.cruzi.CLBrener.Esmeraldo/tree/master/inst/extdata>,
it seems like there should be a straight-forward way to feed this into a
AnnotationHub recipe. Is that the right approach to take?

Any help or suggestions would be greatly appreciated.

Thanks!
Keith

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