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Configure Library Paths and Environment Variables for Beethoven Workflow

Source: R/set_arguments.R
sys_beethoven.Rd

This function sets up the library paths and environmental variables required for running the Beethoven workflow in a containerized environment.

Usage

sys_beethoven(
  libpaths = .libPaths(grep(paste0("biotools|", Sys.getenv("USER")), .libPaths(), value =
    TRUE, invert = TRUE)),
  path = paste0("/usr/local/cuda/bin:", "/usr/local/nvidia/bin:", "/usr/local/cuda/bin:",
    "/usr/local/sbin:", "/usr/local/bin:", "/usr/sbin:", "/usr/bin:", "/sbin:", "/bin"),
  ld_library_path = "/usr/local/cuda/lib64",
  cuda_home = "/usr/local/cuda"
)

Arguments

libpaths

A character vector specifying the library paths to use. By default, it excludes user-specific and host paths from .libPaths().

path

A character string specifying the system PATH environment variable. Defaults to a container-friendly configuration with CUDA paths.

ld_library_path

A character string specifying the LD_LIBRARY_PATH environment variable. Defaults to "/usr/local/cuda/lib64".

cuda_home

A character string specifying the CUDA_HOME environment variable. Defaults to "/usr/local/cuda".