[Bioc-devel] Moving from MakeOrganismPackage to AnnotationHub recipes

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Fri Nov 6 16:27:52 CET 2015

Hi Keith,

Yes, we can add your packages to AnnotationHub. I can help with this
process but it would be easier to take the detailed discussion off-line.
I'll look at your links below and get back to you with next steps.

As an fyi, Laurent Gatto added some proteomics data to AnnotationHub
last devel cycle. Code and vignettes are captured here:



On 11/05/2015 12:22 PM, Keith Hughitt wrote:
> 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
> 	[[alternative HTML version deleted]]
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