pcl: add_ccs2csv, pb-lite-driver: Update

pubchemlite/R/add_ccs2csv.R

@@ -15,7 +15,7 @@ SEL_ADDUCTS <- NULL # Change to adducts needed, if a subset of adducts
 
 dir_start <- Sys.getenv("STARTDIR")
 args <- commandArgs(trailingOnly = T)
-fn_config <- args[[1]]
+fn_config <- file.path(dir_start,args[[1]])
 if (!file.exists(fn_config)) stop("Config file", fn_config," does not exist.")
 x <- yaml::yaml.load_file(fn_config)
 fn_ccs <- file.path(dir_start,x$ccs_src_path)

pubchemlite/pb-lite-driver.sh

 declare -gx INPUTDIR
+declare -gx STARTDIR="$PWD"
 declare -agx ALL_STAGES=( "cleanup" "prepare" "fetch_scripts_sources" "build" "quotes" "buildccs" "sanity_postbuild" "eval4pub" "epilog")
 declare -a STAGES
 STAGES=() 			# Which stages should be run.
@@ -125,7 +126,8 @@ function build() {
 
 function buildccs() {
     header BUILDCCS
-    (export STARTDIR="$PWD";cd "$WORKDIR"; Rscript --vanilla "${SCRIPTDIR}/R/add_ccs2csv.R" "$STARTDIR/$MANIF" "$WORKDIR/$OUTMFFILE" "$WORKDIR/$OUTMFCCSFILE")
+    (cd "$WORKDIR"; Rscript --vanilla "${SCRIPTDIR}/R/add_ccs2csv.R" "$MANIF" "$WORKDIR/$OUTMFFILE" "$WORKDIR/$OUTMFCCSFILE")
+    # (export STARTDIR="$PWD";cd "$WORKDIR"; Rscript --vanilla "${SCRIPTDIR}/R/add_ccs2csv.R" "$STARTDIR/$MANIF" "$WORKDIR/$OUTMFFILE" "$WORKDIR/$OUTMFCCSFILE")
     footer BUILDCCS
 }