initialize hail, using more options — hail_init • BiocHail

initialize hail, using more options

Usage

hail_init(
  quiet = FALSE,
  min_block_size = 0L,
  branching_factor = 50L,
  default_reference = "GRCh37",
  global_seed = 1234L,
  log = tempfile(),
  spark_conf = NULL,
  gcs_requester_pays_configuration = NULL
)

Arguments

quiet: logical(1) defaults to FALSE
min_block_size: integer(1) defaults to 0L
branching_factor: integer(1) defaults to 50L
default_reference: character(1) defaults to "GRCh37", for compatibility with earlier `hail_init`
global_seed: integer(1) defaults to 1234L
log: character(1) target folder for logging, defaults to tempfile()
spark_conf: list, defaults to NULL
gcs_requester_pays_configuration: list, defaults to NULL

Value

python reference to hail module

Note

hail object may be passed around. See hail documentation for details on all args.

Examples

proj = Sys.getenv("GOOGLE_PROJECT")
buck = Sys.getenv("GCS_BUCKET")
if (nchar(buck)>0) {
  # conf = list(proj, c(buck)) doesn't seem to generate tuple[str,Sequence[str]]
  hl <- hail_init()   #gcs_requester_pays_configuration=conf)
  hl$default_reference()
}