bare interface to hail using reticulate

Usage

bare_hail()

Value

python reference to hail module

Note

`/home/jupyter/.local/share/r-miniconda/envs/r-reticulate/bin/pip3 install...` is used to ensure that reticulate's python ecosystem is what we want

`bare_hail()$init(idempotent=TRUE)` should be run

Examples

# assumes terra
if (nchar(Sys.getenv("WORKSPACE_NAMESPACE"))>0) {
  hl = bare_hail()
  hl$init(idempotent=TRUE, spark_conf=list(
      'spark.hadoop.fs.gs.requester.pays.mode'= 'CUSTOM',
      'spark.hadoop.fs.gs.requester.pays.buckets'= 'ukb-diverse-pops-public',
      'spark.hadoop.fs.gs.requester.pays.project.id'= Sys.getenv("GOOGLE_PROJECT")))
  hl$read_matrix_table('gs://ukb-diverse-pops-public/sumstats_release/results_full.mt')$describe()
  if (FALSE) { # \dontrun{
  # this is supposed to get us some LD data but xx.shape fails, issue filed
    hli = reticulate::import("hail.linalg")
    upa = reticulate::import("ukbb_pan_ancestry")
    xx = hli$BlockMatrix$read(upa$get_ld_matrix_path('AFR'))
   } # }
  }