Unverified Commit d244e837 authored by Todor Kondic's avatar Todor Kondic
Browse files

pcl: add_ccs2csv, pb-lite-driver: Update

parent 2020e7d5
......@@ -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$ccs_src_path)
......
declare -gx INPUTDIR
declare -gx STARTDIR="$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
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment