make_eupath_bsgenome: Generate a BSgenome package from the eupathdb.

In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

Generate a BSgenome package from the eupathdb.

Description

Since we go to the trouble to try and generate nice orgdb/txdb/organismdbi packages, it seems to me that we ought to also be able to make a readable genome package. I should probably use some of the logic from this to make the organismdbi generator smarter.

Usage

make_eupath_bsgenome(
  entry,
  eu_version = NULL,
  build_dir = "build",
  copy_s3 = FALSE,
  install = TRUE,
  reinstall = FALSE,
  author = NULL,
  verbose = FALSE,
  build = TRUE
)

Arguments

entry	Single eupathdb metadata entry.
eu_version	Which version of the eupathdb to use for creating the BSGenome?
build_dir	Working directory.
copy_s3	Copy the 2bit file into an s3 staging directory for copying to AnnotationHub?
install	Install the resulting package?
reinstall	Rewrite an existing package directory.
...	Extra arguments for downloading metadata when not provided.

Value

List of package names generated (only 1).

Author(s)

atb

khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.