## ----style, echo = FALSE, results = 'asis'---------------- BiocStyle::markdown() options(width=60, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), tidy.opts=list(width.cutoff=60), tidy=TRUE) ## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE---- suppressPackageStartupMessages({ library(systemPipeR) library(systemPipeRdata) library(BiocGenerics) }) ## ----install, eval=FALSE---------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("systemPipeRdata") # Installs from Bioconductor once # # available there # BiocManager::install("tgirke/systemPipeR", build_vignettes=TRUE, # dependencies=TRUE) # Installs from github ## ----load_systemPipeRdata, eval=TRUE---------------------- library("systemPipeRdata") # Loads the package ## ----documentation_systemPipeRdata, eval=FALSE------------ # library(help="systemPipeRdata") # Lists package info # vignette("systemPipeRdata") # Opens vignette ## ----generate_workenvir, eval=FALSE----------------------- # genWorkenvir(workflow="varseq", mydirname=NULL, url=NULL, urlname=NULL) # setwd("varseq") ## ----load_systemPipeR, eval=TRUE, messages=FALSE---------- library("systemPipeR") # Loads systemPipeR which needs to be installed via BiocManager::install() from Bioconductor ## ----documentation_systemPipeR, eval=FALSE---------------- # vignette("systemPipeR", package = "systemPipeR") ## ----return_samplepaths, eval=TRUE------------------------ pathList() ## ----sessionInfo------------------------------------------ sessionInfo()