cli: Install or check the command line interface scripts.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Install or check the command line interface scripts.

Description

The scripts (scdrake shell script and scdrake.R) are bundled with the scdrake package and their paths can be retrieved with:

system.file("scdrake", package = "scdrake", mustWork = TRUE)
system.file("scdrake.R", package = "scdrake", mustWork = TRUE)

check_cli() is checking the presence of the scdrake CLI script in the PATH environment variable, and whether the command ⁠$ scdrake -h⁠ finishes successfully.

Usage

install_cli(
  dir = NULL,
  type = c("user", "system"),
  ask = TRUE,
  verbose = TRUE,
  .dry = FALSE
)

check_cli(verbose = TRUE)

Arguments

dir	A character scalar: path to directory where scripts will be copied to. If NULL, the path will be determined based on type.
type	A character scalar: For "user": install into the user's home directory under .local/bin For "system": install into ⁠/usr/local/bin⁠
ask	A logical scalar: if TRUE, ask before copying.
verbose	A logical scalar: if TRUE, be verbose.
.dry	A logical scalar: if TRUE, don't copy the files and just return output paths.

Value

install_cli(): invisibly a character vector of length two: paths to installed files.

check_cli(): invisibly TRUE when the checks are successful, FALSE otherwise.

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.