set_tools: Function to generate tools path object

In JhuangLab/ngstk: Next-Generation Sequencing (NGS) Data Analysis Toolkit

Description

Function to generate tools path object

Usage

set_tools(config.file = "", config.list = list(), config.vec = c(),
  eval.params = list())

Arguments

config.file	Path of tools configuration file (json, ini, yaml and toml be supported)
config.list	List object of tools that all of tools path (exclude those without names).
config.vec	Vector object of tools that all of tools path (exclude those without names).
eval.params	Params pass to configr::eval.config

Value

List object contain the tools path that can be used by other function in ngstk package

Examples

config.file <- system.file('extdata', 'demo/tools_config.json', package = 'ngstk')
config.list <- list(gatk = '/path/gatk')
config.vec <- c('/path/samtools')
names(config.vec) <- 'samtools'
tools <- set_tools(config.file, config.list, config.vec,
                  eval.params = list(config = 'tools'))

JhuangLab/ngstk documentation built on May 28, 2019, 12:43 p.m.