fix: put back code for getting bind paths from config

charlie

@@ -364,7 +364,16 @@ function unlock() {
 function set_singularity_binds(){
   # this functions tries find what folders to bind
   # TODO parse config file with pyyaml to determine singularity bind paths
-  SINGULARITY_BINDS="-B $EXTRA_SINGULARITY_BINDS,$PIPELINE_HOME,$WORKDIR"
+  echo "$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)}')
+  SINGULARITY_BINDS="-B $EXTRA_SINGULARITY_BINDS,$binds"
 }
 
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