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

pubchemlite/R/add_ccs2csv.R

@@ -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]]
 

pubchemlite/pb-lite-driver.sh

@@ -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
 }