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Use a native (no-container) MitoPilot environment in this R session

Source: R/native_env.R
native_setup.Rd

Applies the PATH and variables from `<prefix>/activate.sh` (written by `inst/native/install_mitopilot_native.sh`) to the current session, so `nextflow`, `java`, and every pipeline tool resolve here exactly as they do inside pipeline tasks. Call it once after `library(MitoPilot)` when running the app from RStudio Server or any R session that was not started from a shell where `activate.sh` was already sourced. The app itself reads the same file from the project `.config`, so this is only needed for console use.

Usage

native_setup(prefix = Sys.getenv("MITOPILOT_NATIVE_PREFIX"))

Arguments

prefix

Directory given to `install_mitopilot_native.sh –prefix`. Defaults to `MITOPILOT_NATIVE_PREFIX` if set.

Value

(invisibly) `TRUE`.