## ----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(systemPipeRdata) }) ## ----install, eval=FALSE---------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("systemPipeRdata") ## ----install_devel, eval=FALSE---------------------------- # BiocManager::install("systemPipeRdata", version = "devel", build_vignettes=TRUE, # dependencies=TRUE) # Installs Devel version from Bioconductor ## ----load_systemPipeRdata, eval=TRUE, messages=FALSE, warnings=FALSE---- 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="systemPipeR/SPrnaseq", mydirname="rnaseq") # setwd("rnaseq") ## ----project_rnaseq, eval=FALSE--------------------------- # sal <- SPRproject() # sal <- importWF(sal, file_path = "systemPipeVARseq.Rmd", verbose = FALSE) ## ----run_rnaseq, eval=FALSE------------------------------- # sal <- runWF(sal) ## ----plot_rnaseq, eval=FALSE------------------------------ # plotWF(sal) ## ----report_rnaseq, eval=FALSE---------------------------- # sal <- renderLogs(sal) ## ----reporttech_rnaseq, eval=FALSE------------------------ # sal <- renderReport(sal) ## ----eval=FALSE, tidy=FALSE------------------------------- # availableWF(github = TRUE) ## ----eval=FALSE, tidy=FALSE------------------------------- # genWorkenvir(workflow="systemPipeR/SPrnaseq", mydirname="NULL") # setwd("SPrnaseq") ## ----eval=FALSE, tidy=FALSE------------------------------- # genWorkenvir(workflow="systemPipeR/SPrnaseq", ref = "singleMachine") # setwd("SPrnaseq") ## ----eval=FALSE, tidy=FALSE------------------------------- # genWorkenvir(workflow="systemPipeR/SPrnaseq", url = "https://raw.githubusercontent.com/systemPipeR/systemPipeRNAseq/cluster/vignettes/systemPipeRNAseq.Rmd", # urlname = "rnaseq_V-cluster.Rmd") # setwd("rnaseq") ## ----return_samplepaths, eval=TRUE------------------------ pathList()[1:2] ## ----sessionInfo------------------------------------------ sessionInfo()