From c82d42aa3bf33b47551df2e48a7b023f71c410c6 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 16 Oct 2024 16:59:54 -0400
Subject: [PATCH] chore: delete deprecated code

---
 charlie | 17 +----------------
 1 file changed, 1 insertion(+), 16 deletions(-)

diff --git a/charlie b/charlie
index 0563761..3e35138 100755
--- a/charlie
+++ b/charlie
@@ -355,21 +355,6 @@ function unlock() {
 # SET SINGULARITY BINDS ... bind required singularity folders appropriately
 ##########################################################################################
 
-function set_singularity_binds_bash(){
-  # this functions tries find what folders to bind
-  # TODO parse config file with pyyaml to determine singularity bind paths
-  echo "$PIPELINE_HOME" > ${WORKDIR}/tmp1
-  echo "$WORKDIR" >> ${WORKDIR}/tmp1
-  grep -o '\/.*' <(cat ${WORKDIR}/config.yaml ${WORKDIR}/samples.tsv)|dos2unix|tr '\t' '\n'|grep -v ' \|\/\/'|sort|uniq >> ${WORKDIR}/tmp1
-  grep gpfs ${WORKDIR}/tmp1|awk -F'/' -v OFS='/' '{print $1,$2,$3,$4,$5}'| grep "[a-zA-Z0-9]" |sort|uniq > ${WORKDIR}/tmp2
-  grep -v gpfs ${WORKDIR}/tmp1|awk -F'/' -v OFS='/' '{print $1,$2,$3}'| grep "[a-zA-Z0-9]"|sort|uniq > ${WORKDIR}/tmp3
-  while read a;do readlink -f $a;done < ${WORKDIR}/tmp3 | grep "[a-zA-Z0-9]"> ${WORKDIR}/tmp4
-  binds=$(cat ${WORKDIR}/tmp2 ${WORKDIR}/tmp3 ${WORKDIR}/tmp4|sort|uniq |tr '\n' ',')
-  rm -f ${WORKDIR}/tmp?
-  binds=$(echo $binds|awk '{print substr($1,1,length($1)-1)}' | sed -s 's/"//g' | sed -s "s/'//g")
-  SINGULARITY_BINDS="-B $EXTRA_SINGULARITY_BINDS,$binds"
-}
-
 function set_singularity_binds() {
   binds=$( $PIPELINE_HOME/workflow/scripts/set_singularity_bind_paths.py ${WORKDIR}/config.yaml ${WORKDIR}/samples.tsv)
   SINGULARITY_BINDS="-B $EXTRA_SINGULARITY_BINDS,$binds"
@@ -646,7 +631,7 @@ function main(){
       ;;
   esac
   done
-  #WORKDIR=$(readlink "$WORKDIR")
+
   echo "Working Dir: $WORKDIR"
 
   if [[ -z "$SING_CACHE_DIR" ]]; then