Unverified Commit 7521c18f authored by Todor Kondic's avatar Todor Kondic
Browse files

pcl: R: add_ccs2csv: Update; pb-lite-driver: Update stage buildccs

parent abd67334
......@@ -13,12 +13,12 @@ SEL_ADDUCTS <- NULL # Change to adducts needed, if a subset of adducts
# desired. Otherwise, all shall be returned.
dir_start <- Sys.getenv("$STARTDIR")
args <- commandArgs(trailingOnly = T)
fn_config <- args[[1]]
if (!file.exists(fn_config)) stop("Config file", fn_config," does not exist.")
x <- yaml::yaml.load_file(fn_config)
fn_ccs <- x$ccs_src_path
fn_ccs <- file.path(dir_start,x$ccs_src_path)
fn_mf_csv <- args[[2]]
fn_mf_res_csv <- args[[3]]
......
......@@ -125,7 +125,7 @@ function build() {
function buildccs() {
header BUILDCCS
(THEPWD="$PWD";cd "$WORKDIR"; Rscript --vanilla "${SCRIPTDIR}/R/add_ccs2csv.R" "$THEPWD/$MANIF" "$WORKDIR/$OUTMFFILE" "$WORKDIR/$OUTMFCCSFILE")
(STARTDIR="$PWD";cd "$WORKDIR"; Rscript --vanilla "${SCRIPTDIR}/R/add_ccs2csv.R" "$STARTDIR/$MANIF" "$WORKDIR/$OUTMFFILE" "$WORKDIR/$OUTMFCCSFILE")
footer BUILDCCS
}
......
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