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Configure Conda Environment for csMR

csMR_env.Rd

csMR_env() prepares the official csMR environment. It clones the official repository if missing, tries envs/envpy3.yml first, falls back to a temporary compatibility env file only when the official file cannot solve, installs required R packages into the csMR conda library, checks PLINK 1.90, and returns the runtime paths required by the csMR README.

Usage

csMR_env(
  repo_dir = "~/Project/software/csMR",
  repo_url = "https://github.com/rhhao/csMR.git",
  env_name = "csMR",
  conda = Sys.which("conda"),
  mamba = Sys.which("mamba"),
  plink_path = Sys.which("plink"),
  ref = "main",
  overwrite = FALSE
)

Arguments

repo_dir

Path to the csMR repository.

repo_url

Official csMR GitHub URL.

env_name

Conda environment name.

conda

Path to conda.

mamba

Path to mamba.

Optional PLINK 1.90 path. If empty, PATH and plinkbinr::get_plink_exe() are tried.

ref

Git branch or tag.

overwrite

Whether to rebuild an existing env.

Value

A list with repo_dir, env_name, env_prefix, env_file, r_home, r_library, and plink.

Examples

if (FALSE) { # \dontrun{
cfg <- csMR_env()
cfg$r_library
} # }