cwlInstall

To source Rcwl scripts

cwlInstall(rname, bfc = NULL, env = .GlobalEnv)

Arguments

rname	The name or filepath of tool or pipeline to install (`rname` or `fpath` column from the `bfc` object returned from `cwlSearch`).
bfc	The `BiocFileCache` object for the recipes returned from `cwlUpdate`. The default is NULL which automatically detect the "Rcwl" cache directory.
env	The R enviroment to export to. The default is `.GlobalEnv`.

Details

Note to developers that the dependent Rcwl scripts should be included in the recipe with `@include` tag.

Examples

if (FALSE) {
tls <- cwlSearch("bwa")
tls$rname
cwlInstall("tl_bwa")
cwlInstall(tls$fpath[tls$rname == "tl_bwa"])  ## equivalent
bwa
}