## ----setup, echo=FALSE, results="hide", include = FALSE------------------------------------------- knitr::opts_chunk$set(tidy=FALSE, cache=FALSE, #dev="png", message=FALSE, error=FALSE, warning=TRUE) options(width=100) ## ----getPackage, eval=FALSE----------------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("Herper") ## ------------------------------------------------------------------------------------------------- library(Herper) ## ----install_Condatools, echo=T, eval=F----------------------------------------------------------- # myMiniconda <- file.path(tempdir(),"Test") # install_CondaTools("salmon==1.3.0", "herper", pathToMiniConda = myMiniconda) ## ----install_CondaSysReqs, eval=F----------------------------------------------------------------- # testPkg <- system.file("extdata/HerperTestPkg",package="Herper") # install.packages(testPkg,type = "source",repos = NULL) # condaDir <- file.path(tempdir(),"r-miniconda") # condaPaths <- install_CondaSysReqs("HerperTestPkg", pathToMiniConda = myMiniconda,SysReqsAsJSON=FALSE) # #' system2(file.path(condaPaths$pathToEnvBin,"samtools"),args = "--help") # ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()