install_CondaSysReqs {Herper} | R Documentation |
Install Conda requirements
install_CondaSysReqs( pkg, channels = NULL, env = NULL, pathToMiniConda = NULL, updateEnv = FALSE, SysReqsAsJSON = FALSE, SysReqsSep = ",", verbose = FALSE )
pkg |
Package to install Conda System Requirements from. |
channels |
Additional channels for miniconda (bioconda defaults and conda-forge are included automatically) |
env |
Name of Conda environment to install tools into. |
pathToMiniConda |
NULL Path to miniconda installation |
updateEnv |
Update existing package's conda environment if already installed. |
SysReqsAsJSON |
Parse the SystemRequirements in JSON format (see Details). Default is TRUE. |
SysReqsSep |
Separator used in SystemRequirement field. |
verbose |
Print messages on progress (Default is FALSE). |
Nothing returned. Output written to file.
Thomas Carroll
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 = condaDir, SysReqsAsJSON = FALSE) system2(file.path(condaPaths$pathToEnvBin, "samtools"), args = "--help")