diff --git a/CHANGELOG.md b/CHANGELOG.md
index 42f8850..b51ad1c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,9 @@
 ## CHARLIE development version
 
-- Fix bug where CHARLIE was falsely throwing a file permissions error for tempdir values containing bash variables. (#118, @kelly-sovacool)
+### bug fixes
+
+- CHARLIE was falsely throwing a file permissions error for tempdir values containing bash variables. (#118, @kelly-sovacool)
+- Singularity bind paths were not being set properly. (#119, @kelly-sovacool)
 
 ## CHARLIE 0.11.0
 
diff --git a/charlie b/charlie
index 6e324b8..ca9e827 100755
--- a/charlie
+++ b/charlie
@@ -220,7 +220,8 @@ sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" \
     -e "s/HOST/${HOST}/g" \
     -e "s/ADDITIVES/${ADDITIVES}/g" \
     -e "s/VIRUSES/${VIRUSES}/g" \
-    ${PIPELINE_HOME}/config/$PLATFORM/config.yaml > $CONFIGFILE
+    ${PIPELINE_HOME}/config/$PLATFORM/config.yaml |\
+    cat - ${PIPELINE_HOME}/config/containers.yaml > $CONFIGFILE
 fi
 if [ ! -f $WORKDIR/nclscan.config ];then
 sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" ${PIPELINE_HOME}/resources/NCLscan.config.template > $WORKDIR/nclscan.config
@@ -293,7 +294,9 @@ function reconfig(){
   # rebuild config file and replace the config.yaml in the WORKDIR
   # this is only for dev purposes when new key-value pairs are being added to the config file
   check_essential_files
-  sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" ${PIPELINE_HOME}/config/config.yaml > $WORKDIR/config.yaml
+  sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" \
+  ${PIPELINE_HOME}/config/config.yaml |\
+  cat - ${PIPELINE_HOME}/config/containers.yaml > $WORKDIR/config.yaml
   echo "$WORKDIR/config.yaml has been updated!"
 }
 
@@ -355,21 +358,10 @@ function unlock() {
 # SET SINGULARITY BINDS ... bind required singularity folders appropriately
 ##########################################################################################
 
-function set_singularity_binds(){
-  # 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($1)-1)}')
+function set_singularity_binds() {
+  binds=$( $PIPELINE_HOME/workflow/scripts/set_singularity_bind_paths.py ${WORKDIR}/config.yaml ${WORKDIR}/samples.tsv)
   SINGULARITY_BINDS="-B $EXTRA_SINGULARITY_BINDS,$binds"
 }
-
 ##########################################################################################
 # PRINT SINGULARITY BINDS ... print bound singularity folders for debugging
 ##########################################################################################
@@ -642,7 +634,7 @@ function main(){
       ;;
   esac
   done
-  WORKDIR=$(readlink -f "$WORKDIR")
+
   echo "Working Dir: $WORKDIR"
 
   if [[ -z "$SING_CACHE_DIR" ]]; then
diff --git a/config/biowulf/config.yaml b/config/biowulf/config.yaml
index da1eb19..c1dfa91 100644
--- a/config/biowulf/config.yaml
+++ b/config/biowulf/config.yaml
@@ -4,7 +4,7 @@
 workdir: "WORKDIR"
 
 # temporary directory for intermediate files that are not saved
-tempdir: '/lscratch/$SLURM_JOB_ID'
+tempdir: "/lscratch/$SLURM_JOB_ID"
 
 # tab delimited samples file ... should have the following 3 columns
 # sampleName	path_to_R1_fastq	path_to_R2_fastq
@@ -112,20 +112,3 @@ fastas_gtfs_dir: "/data/CCBR_Pipeliner/db/PipeDB/charlie/fastas_gtfs"
 annotation_lookups:
   hg38: "PIPELINE_HOME/resources/hg38_2_hg19_lookup.txt"
   mm39: "PIPELINE_HOME/resources/mm39_circBase_annotation_lookup.txt"
-
-containers:
-  base: "docker://nciccbr/ccbr_ubuntu_base_20.04:v6"
-  bowtie1: "docker://nciccbr/charlie_bowtie1:v0.1.0"
-  circexplorer: "docker://nciccbr/ccbr_circexplorer:v1.0"
-  circRNA_finder: "docker://nciccbr/charlie_circrna_finder:v1"
-  ciri: "docker://nciccbr/charlie_ciri2:v1"
-  clear: "docker://nciccbr/ccbr_clear:2"
-  cutadapt: "docker://nciccbr/charlie_cutadapt_fqfilter:v1"
-  dcc: "docker://nciccbr/charlie_dcc:v0.2.0"
-  fastqc: "docker://nciccbr/ccrgb_qctools:v4.0"
-  mapsplice: "docker://cgrlab/mapsplice2:latest"
-  multiqc: "docker://nciccbr/ccbr_multiqc_1.15:v1"
-  picard: "docker://nciccbr/ccbr_picard_2.27.5:v1"
-  R: "docker://nciccbr/ccbr_r_4.3.0:v1"
-  star: "docker://nciccbr/ccbr_star_2.7.6a:latest"
-  star_ucsc_cufflinks: "docker://nciccbr/charlie_star_ucsc_cufflinks:v0.4.0"
diff --git a/config/containers.yaml b/config/containers.yaml
new file mode 100644
index 0000000..baca596
--- /dev/null
+++ b/config/containers.yaml
@@ -0,0 +1,16 @@
+containers:
+  base: "docker://nciccbr/ccbr_ubuntu_base_20.04:v6"
+  bowtie1: "docker://nciccbr/charlie_bowtie1:v0.1.1"
+  circexplorer: "docker://nciccbr/ccbr_circexplorer:v1.0"
+  circRNA_finder: "docker://nciccbr/charlie_circrna_finder:v1.0.1"
+  ciri: "docker://nciccbr/charlie_ciri2:v1.0.1"
+  clear: "docker://nciccbr/ccbr_clear:v2.0.1"
+  cutadapt: "docker://nciccbr/charlie_cutadapt_fqfilter:v1.0.1"
+  dcc: "docker://nciccbr/charlie_dcc:v0.2.1"
+  fastqc: "docker://nciccbr/ccrgb_qctools:v4.0"
+  mapsplice: "docker://cgrlab/mapsplice2:latest"
+  multiqc: "docker://nciccbr/ccbr_multiqc_1.15:v1"
+  picard: "docker://nciccbr/ccbr_picard_2.27.5:v1"
+  R: "docker://nciccbr/ccbr_r_4.3.0:v1"
+  star: "docker://nciccbr/ccbr_star_2.7.6a:latest"
+  star_ucsc_cufflinks: "docker://nciccbr/charlie_star_ucsc_cufflinks:v0.4.1"
diff --git a/config/fnlcr/config.yaml b/config/fnlcr/config.yaml
index de47366..86e0f40 100644
--- a/config/fnlcr/config.yaml
+++ b/config/fnlcr/config.yaml
@@ -112,20 +112,3 @@ fastas_gtfs_dir: "/mnt/projects/CCBR-Pipelines/db/charlie/fastas_gtfs"
 annotation_lookups:
   hg38: "PIPELINE_HOME/resources/hg38_2_hg19_lookup.txt"
   mm39: "PIPELINE_HOME/resources/mm39_circBase_annotation_lookup.txt"
-
-containers:
-  base: "docker://nciccbr/ccbr_ubuntu_base_20.04:v6"
-  bowtie1: "docker://nciccbr/charlie_bowtie1:v0.1.0"
-  circexplorer: "docker://nciccbr/ccbr_circexplorer:v1.0"
-  circRNA_finder: "docker://nciccbr/charlie_circrna_finder:v1"
-  ciri: "docker://nciccbr/charlie_ciri2:v1"
-  clear: "docker://nciccbr/ccbr_clear:2"
-  cutadapt: "docker://nciccbr/charlie_cutadapt_fqfilter:v1"
-  dcc: "docker://nciccbr/charlie_dcc:v0.2.0"
-  fastqc: "docker://nciccbr/ccrgb_qctools:v4.0"
-  mapsplice: "docker://cgrlab/mapsplice2:latest"
-  multiqc: "docker://nciccbr/ccbr_multiqc_1.15:v1"
-  picard: "docker://nciccbr/ccbr_picard_2.27.5:v1"
-  R: "docker://nciccbr/ccbr_r_4.3.0:v1"
-  star: "docker://nciccbr/ccbr_star_2.7.6a:latest"
-  star_ucsc_cufflinks: "docker://nciccbr/charlie_star_ucsc_cufflinks:v0.4.0"
diff --git a/docker/bowtie1/Dockerfile b/docker/bowtie1/Dockerfile
index 6386538..3cea9ee 100644
--- a/docker/bowtie1/Dockerfile
+++ b/docker/bowtie1/Dockerfile
@@ -12,6 +12,8 @@ ENV REPONAME=${REPONAME}
 COPY environment.txt /data2/
 RUN mamba install -c conda-forge -c bioconda --file /data2/environment.txt
 ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+ENV PATH="/opt2/conda/bin/:$PATH"
+ENV PYTHONPATH=""
 
 # Save Dockerfile in the docker
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
diff --git a/docker/bowtie1/meta.yml b/docker/bowtie1/meta.yml
index 0baf464..0ad8002 100644
--- a/docker/bowtie1/meta.yml
+++ b/docker/bowtie1/meta.yml
@@ -1,4 +1,4 @@
 dockerhub_namespace: nciccbr
 image_name: charlie_bowtie1
-version: v0.1.0
+version: v0.1.1
 container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/docker/circRNA_finder/Dockerfile b/docker/circRNA_finder/Dockerfile
index 0262596..97014f2 100644
--- a/docker/circRNA_finder/Dockerfile
+++ b/docker/circRNA_finder/Dockerfile
@@ -12,6 +12,8 @@ ENV REPONAME=${REPONAME}
 COPY environment.txt /data2/
 RUN mamba install -c conda-forge -c bioconda --file /data2/environment.txt
 ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+ENV PATH="/opt2/conda/bin/:$PATH"
+ENV PYTHONPATH=""
 
 # install circRNA_finder
 WORKDIR /opt2
diff --git a/docker/circRNA_finder/meta.yml b/docker/circRNA_finder/meta.yml
index ae5bcb3..2810384 100644
--- a/docker/circRNA_finder/meta.yml
+++ b/docker/circRNA_finder/meta.yml
@@ -1,4 +1,4 @@
 dockerhub_namespace: nciccbr
 image_name: charlie_circrna_finder
-version: v1
+version: v1.0.1
 container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/docker/ciri2/Dockerfile b/docker/ciri2/Dockerfile
index c8ed18e..982884c 100644
--- a/docker/ciri2/Dockerfile
+++ b/docker/ciri2/Dockerfile
@@ -13,6 +13,7 @@ WORKDIR /opt2
 RUN wget -O CIRI.zip https://sourceforge.net/projects/ciri/files/CIRI2/CIRI_v2.0.6.zip/download && \
     unzip CIRI.zip
 ENV PATH="/opt2/CIRI2_v2.0.6/:$PATH"
+ENV PYTHONPATH="/usr/local/lib/python3.8/dist-packages/"
 
 # Save Dockerfile in the docker
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
diff --git a/docker/ciri2/meta.yml b/docker/ciri2/meta.yml
index 65fe3ed..7996d83 100644
--- a/docker/ciri2/meta.yml
+++ b/docker/ciri2/meta.yml
@@ -1,4 +1,4 @@
 dockerhub_namespace: nciccbr
 image_name: charlie_ciri2
-version: v1
+version: v1.0.1
 container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/docker/clear/Dockerfile b/docker/clear/Dockerfile
index 9f53a10..1257399 100755
--- a/docker/clear/Dockerfile
+++ b/docker/clear/Dockerfile
@@ -11,6 +11,7 @@ ENV CONDA_ENV=clear
 RUN mamba env create -n ${CONDA_ENV} -f /data2/environment.yml && \
     echo "conda activate ${CONDA_ENV}" > ~/.bashrc
 ENV PATH="/opt2/conda/envs/${CONDA_ENV}/bin:$PATH"
+ENV PYTHONPATH="/opt2/conda/envs/${CONDA_ENV}/lib/${CONDA_ENV}/site-packages/"
 RUN python -m pip install git+https://github.com/YangLab/CLEAR.git
 RUN which circ_quant && circ_quant -h
 
diff --git a/docker/clear/meta.yml b/docker/clear/meta.yml
index b04cd5d..d4c03a7 100644
--- a/docker/clear/meta.yml
+++ b/docker/clear/meta.yml
@@ -1,4 +1,4 @@
 dockerhub_namespace: nciccbr
 image_name: ccbr_clear
-version: 2
+version: v2.0.1
 container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/docker/cutadapt_fqfilter/Dockerfile b/docker/cutadapt_fqfilter/Dockerfile
index de3475e..23426c1 100644
--- a/docker/cutadapt_fqfilter/Dockerfile
+++ b/docker/cutadapt_fqfilter/Dockerfile
@@ -14,6 +14,7 @@ ENV CONDA_ENV=cutadapt
 RUN mamba env create -n ${CONDA_ENV} -f /data2/environment.yml && \
     echo "conda activate ${CONDA_ENV}" > ~/.bashrc
 ENV PATH="/opt2/conda/envs/${CONDA_ENV}/bin:$PATH"
+ENV PYTHONPATH="/opt2/conda/envs/${CONDA_ENV}/lib/${CONDA_ENV}/site-packages/"
 ENV R_LIBS_USER=/opt2/conda/lib/R/library/
 
 # Save Dockerfile in the docker
diff --git a/docker/cutadapt_fqfilter/meta.yml b/docker/cutadapt_fqfilter/meta.yml
index ed3a6b6..3396e67 100644
--- a/docker/cutadapt_fqfilter/meta.yml
+++ b/docker/cutadapt_fqfilter/meta.yml
@@ -1,4 +1,4 @@
 dockerhub_namespace: nciccbr
 image_name: charlie_cutadapt_fqfilter
-version: v1
+version: v1.0.1
 container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/docker/dcc/Dockerfile b/docker/dcc/Dockerfile
index 6338f48..0f9d30c 100644
--- a/docker/dcc/Dockerfile
+++ b/docker/dcc/Dockerfile
@@ -14,7 +14,9 @@ WORKDIR /opt2
 RUN wget https://github.com/dieterich-lab/DCC/archive/${DCC_VERSION}.zip -O dcc.zip && \
     unzip dcc.zip && \
     cd DCC-${DCC_VERSION} && \
+    pip install numpy==1.21.0 && \
     python setup.py install
+ENV PYTHONPATH="/usr/local/lib/python3.8/dist-packages/"
 RUN which DCC && DCC -h
 
 # Save Dockerfile in the docker
diff --git a/docker/dcc/meta.yml b/docker/dcc/meta.yml
index a3a1393..5caca40 100644
--- a/docker/dcc/meta.yml
+++ b/docker/dcc/meta.yml
@@ -1,4 +1,4 @@
 dockerhub_namespace: nciccbr
 image_name: charlie_dcc
-version: v0.2.0
+version: v0.2.1
 container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/docker/star_ucsc_cufflinks/Dockerfile b/docker/star_ucsc_cufflinks/Dockerfile
index 39ef4e3..b81aa44 100644
--- a/docker/star_ucsc_cufflinks/Dockerfile
+++ b/docker/star_ucsc_cufflinks/Dockerfile
@@ -14,6 +14,7 @@ ENV CONDA_ENV=py3.6
 RUN mamba env create -n ${CONDA_ENV} -f /data2/environment.yml && \
     echo "conda activate ${CONDA_ENV}" > ~/.bashrc
 ENV PATH="/opt2/conda/envs/${CONDA_ENV}/bin:$PATH"
+ENV PYTHONPATH="/opt2/conda/envs/${CONDA_ENV}/lib/${CONDA_ENV}/site-packages/"
 ENV R_LIBS_USER=/opt2/conda/lib/R/library/
 
 # install find_circ
diff --git a/docker/star_ucsc_cufflinks/meta.yml b/docker/star_ucsc_cufflinks/meta.yml
index 12f9f38..084bc08 100644
--- a/docker/star_ucsc_cufflinks/meta.yml
+++ b/docker/star_ucsc_cufflinks/meta.yml
@@ -1,4 +1,4 @@
 dockerhub_namespace: nciccbr
 image_name: charlie_star_ucsc_cufflinks
-version: v0.4.0
+version: v0.4.1
 container: "$(dockerhub_namespace)/$(image_name):$(version)"
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 04bb067..22a9a50 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -305,7 +305,7 @@ include: "rules/post_findcircrna_processing.smk"
 
 on_finish_cmd = f"""
 sleep 10
-mkdir -p {WORKDIR}/log && run_jobby_on_snakemake_log {WORKDIR}/snakemake.log | tee {WORKDIR}/log/snakemake.log.jobby | cut -f2,3,18 > {WORKDIR}/log/snakemake.log.jobby.short
+mkdir -p {WORKDIR}/logs/ && run_jobby_on_snakemake_log {WORKDIR}/snakemake.log | tee {WORKDIR}/logs/snakemake.log.jobby | cut -f2,3,18 > {WORKDIR}/logs/snakemake.log.jobby.short
 if command -v spooker &> /dev/null; then
     spooker {WORKDIR} CHARLIE
 else
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
index 47f06cf..1b408a6 100644
--- a/workflow/rules/align.smk
+++ b/workflow/rules/align.smk
@@ -244,7 +244,7 @@ rule merge_SJ_tabs:
         """
 set -exo pipefail
 cat {input} | \\
-python {params.script1} \\
+python -E {params.script1} \\
     --regions {params.regions} \\
     --filter1regions {params.filter1regions} \\
     --filter1_noncanonical {params.filter1_noncanonical} \\
diff --git a/workflow/rules/create_index.smk b/workflow/rules/create_index.smk
index 419c036..949d6af 100644
--- a/workflow/rules/create_index.smk
+++ b/workflow/rules/create_index.smk
@@ -33,13 +33,13 @@ samtools faidx {params.reffa} && \\
 # bwa index -p ref {params.reffa} > bwa_index.log ... created in a separate rule
 
 # NCLscan files
-python {params.script3} --ingtf {params.refgtf} --outgtf {output.fixed_gtf}
+python -E {params.script3} --ingtf {params.refgtf} --outgtf {output.fixed_gtf}
 gffread -w {output.transcripts_fa} -g {params.reffa} {output.fixed_gtf}
 touch {output.lncRNA_transcripts_fa}
 create_reference.py -c {params.nclscan_config}
 
 gtfToGenePred -ignoreGroupsWithoutExons {output.fixed_gtf} ref.genes.genepred && \\
-    python {params.script1} {output.fixed_gtf} ref.genes.genepred > {output.genepred_w_geneid}
+    python -E {params.script1} {output.fixed_gtf} ref.genes.genepred > {output.genepred_w_geneid}
 
 stardir=$(dirname {output.sa})
 mkdir -p $stardir && \\
@@ -125,4 +125,4 @@ set -exo pipefail
 refdir=$(dirname {params.reffa})
 cd $refdir
 bowtie-build {params.reffa} ref
-"""  
+"""
diff --git a/workflow/rules/findcircrna.smk b/workflow/rules/findcircrna.smk
index 7edec8d..84712fe 100644
--- a/workflow/rules/findcircrna.smk
+++ b/workflow/rules/findcircrna.smk
@@ -141,7 +141,7 @@ def get_per_sample_files_to_merge(wildcards):
 # 2. parse the back_spliced_junction BED from above along with known splicing annotations to CircExplorer2 'parse' to create
 #       a. circularRNA_known.txt ... circRNAs around known gene exons
 #       b. low_conf_circularRNA_known.txt .... circRNAs with low confidence
-# 3. parse back_spliced_junction BED along with circularRNA_known.txt and low_conf_circularRNA_known.txt to custom python script
+# 3. parse back_spliced_junction BED along with circularRNA_known.txt and low_conf_circularRNA_known.txt to custom python -E script
 # to create an aggregated list of BSJs with following columns:
 # | # | ColName     |
 # |---|-------------|
@@ -305,7 +305,7 @@ perl {params.ciripl} \\
 # samtools view -@{threads} -T {params.reffa} -CS {params.sample}.bwa.sam | samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O CRAM -o {output.ciribam} -
 samtools view -@{threads} -bS {params.sample}.bwa.sam | samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.ciribam} -
 rm -rf {params.sample}.bwa.sam
-python {params.script} \\
+python -E {params.script} \\
     --ciriout {output.ciriout} \\
     --back_spliced_min_reads {params.bsj_min_nreads} \\
     --host "{params.host}" \\
@@ -411,7 +411,7 @@ rule create_ciri_count_matrix:
         """
 set -exo pipefail
 cd {params.outdir}
-python {params.script} {params.lookup} {params.hostID}
+python -E {params.script} {params.lookup} {params.hostID}
 """
 
 
@@ -441,8 +441,8 @@ rule create_circexplorer_count_matrix:
     shell:
         """
 cd {params.outdir}
-python {params.script} {params.lookup} {params.hostID}
-python {params.script2} {params.lookup} {params.hostID}
+python -E {params.script} {params.lookup} {params.hostID}
+python -E {params.script2} {params.lookup} {params.hostID}
 """
 
 
@@ -563,7 +563,7 @@ set -exo pipefail
 find {params.cleardir} -maxdepth 1 -type d -name "quant.txt*" -exec rm -rf {{}} \;
 if [[ "$(cat {input.quantfile} | wc -l)" != "0" ]]
 then
-python {params.script} {params.lookup} {input.quantfile} {params.hostID}
+python -E {params.script} {params.lookup} {input.quantfile} {params.hostID}
 else
 touch {output.annotatedquantfile}
 fi
@@ -722,10 +722,10 @@ ls -alrth {params.tmpdir}
 
 paste {output.cr} {output.linear} | cut -f1-5,9 > {params.tmpdir}/CircRNALinearCount
 
-python {params.script} \\
+python -E {params.script} \\
   --CircCoordinates {output.cc} --CircRNALinearCount {params.tmpdir}/CircRNALinearCount -o {output.ct}
 
-python {params.script2} \\
+python -E {params.script2} \\
     --in_dcc_counts_table {output.ct} \\
     --out_dcc_filtered_counts_table {output.ctf} \\
     --back_spliced_min_reads {params.bsj_min_nreads} \\
@@ -843,7 +843,7 @@ R2fn=$(basename {input.R2})
 zcat {input.R1} > {params.tmpdir}/${{R1fn%.*}}
 zcat {input.R2} > {params.tmpdir}/${{R2fn%.*}}
 
-python $MSHOME/mapsplice.py \\
+python -E $MSHOME/mapsplice.py \\
  -1 {params.tmpdir}/${{R1fn%.*}} \\
  -2 {params.tmpdir}/${{R2fn%.*}} \\
  -c {params.separate_fastas} \\
@@ -862,7 +862,7 @@ else
 R1fn=$(basename {input.R1})
 zcat {input.R1} > {params.tmpdir}/${{R1fn%.*}}
 
-python $MSHOME/mapsplice.py \
+python -E $MSHOME/mapsplice.py \
  -1 {params.tmpdir}/${{R1fn%.*}} \
  -c {params.separate_fastas} \
  -p {threads} \
@@ -934,7 +934,7 @@ rule mapsplice_postprocess:
         """
 set -exo pipefail
 mkdir -p {params.tmpdir}
-python {params.script} \\
+python -E {params.script} \\
     --circularRNAstxt {input.circRNAs} \\
     -o {output.ct} \\
     -fo {output.ctf} \\
@@ -1027,7 +1027,7 @@ results_bn=$(basename {output.result})
 if [ "{params.peorse}" == "PE" ];then
 NCLscan.py -c {params.nclscan_config} -pj {params.sample} -o {params.tmpdir} --fq1 {input.R1} --fq2 {input.R2}
 rsync -az --progress {params.tmpdir}/${{results_bn}} {output.result}
-python {params.script} \\
+python -E {params.script} \\
     --result {output.result} \\
     -o {output.ct} \\
     -fo {output.ctf} \\
@@ -1163,7 +1163,7 @@ rule find_circ:
     shell:
         """
 set -exo pipefail
-python --version
+python -E --version
 which python
 mkdir -p {params.tmpdir}
 cd {params.tmpdir}
@@ -1223,7 +1223,7 @@ grep CIRCULAR {params.tmpdir}/{params.sample}.splice_sites.bed | \\
     > {output.find_circ_bsj_bed}
 
 echo -ne "chrom\\tstart\\tend\\tname\\tn_reads\\tstrand\\tn_uniq\\tuniq_bridges\\tbest_qual_left\\tbest_qual_right\\ttissues\\ttiss_counts\\tedits\\tanchor_overlap\\tbreakpoints\\tsignal\\tstrandmatch\\tcategory\\n" > {output.find_circ_bsj_bed_filtered}
-cat {output.find_circ_bsj_bed} | python {params.collapse_script} | awk -F"\\t" -v m={params.min_reads} -v OFS="\\t" '{{if ($5>=m) {{print}}}}'  \\
+cat {output.find_circ_bsj_bed} | python -E {params.collapse_script} | awk -F"\\t" -v m={params.min_reads} -v OFS="\\t" '{{if ($5>=m) {{print}}}}'  \\
     >> {output.find_circ_bsj_bed_filtered}
 """
 
@@ -1332,7 +1332,7 @@ for f in {input};do
     fi
 done
 
-python {params.script} \\
+python -E {params.script} \\
     --counttablelist $infiles \\
     -o {output.matrix} \\
     --minreads {params.bsj_min_nreads}
diff --git a/workflow/rules/post_findcircrna_processing.smk b/workflow/rules/post_findcircrna_processing.smk
index 192cc23..05fe341 100644
--- a/workflow/rules/post_findcircrna_processing.smk
+++ b/workflow/rules/post_findcircrna_processing.smk
@@ -7,7 +7,7 @@ def get_alignment_stats_input(wildcards):
     d['star2bam']=join(WORKDIR,"results",sample,"STAR2p",sample+"_p2.bam")
     d['star2bam_chimeric']=join(WORKDIR,"results",sample,"STAR2p",sample+"_p2.chimeric.bam")
     d['star2bam_non_chimeric']=join(WORKDIR,"results",sample,"STAR2p",sample+"_p2.non_chimeric.bam")
-    d['filtered_bam']=join(WORKDIR,"results",sample,"circExplorer",sample+".bam")  
+    d['filtered_bam']=join(WORKDIR,"results",sample,"circExplorer",sample+".bam")
     d['linearbam']=join(WORKDIR,"results",sample,"circExplorer",sample+".linear.bam")
     d['splicedbam']=join(WORKDIR,"results",sample,"circExplorer",sample+".spliced.bam")
     d['BSJbam']=join(WORKDIR,"results",sample,"circExplorer",sample+".BSJ.bam")
@@ -108,21 +108,21 @@ python3 {params.scriptse} \\
 
 fi
 
-samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.plusBSJbam} {params.tmpdir}/{params.sample}.BSJ.plus.bam 
-samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.minusBSJbam} {params.tmpdir}/{params.sample}.BSJ.minus.bam 
+samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.plusBSJbam} {params.tmpdir}/{params.sample}.BSJ.plus.bam
+samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.minusBSJbam} {params.tmpdir}/{params.sample}.BSJ.minus.bam
 samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o {output.BSJbam} {params.tmpdir}/{params.sample}.BSJ.bam
 
-for b in {output.plusBSJbam} {output.minusBSJbam} {output.BSJbam} 
+for b in {output.plusBSJbam} {output.minusBSJbam} {output.BSJbam}
 # for b in {output.plusBSJbam} {output.minusBSJbam}
 do
     bash {params.bam2bwscript} $b {params.tmpdir}
 done
 
-for i in $(echo {params.host}|tr ',' ' ');do 
+for i in $(echo {params.host}|tr ',' ' ');do
     samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o ${{outdir}}/{params.sample}.${{i}}.BSJ.bam {params.tmpdir}/{params.sample}.${{i}}.BSJ.bam
     bash {params.bam2bwscript} ${{outdir}}/{params.sample}.${{i}}.BSJ.bam {params.tmpdir}
 done
-for i in $(echo {params.viruses}|tr ',' ' ');do 
+for i in $(echo {params.viruses}|tr ',' ' ');do
     samtools sort -l 9 -T {params.tmpdir} --write-index -@{threads} -O BAM -o ${{outdir}}/{params.sample}.${{i}}.BSJ.bam {params.tmpdir}/{params.sample}.${{i}}.BSJ.bam
     bash {params.bam2bwscript} ${{outdir}}/{params.sample}.${{i}}.BSJ.bam {params.tmpdir}
 done
@@ -253,9 +253,6 @@ rm -rf {params.tmpdir}
 # linear_spliced_BSJ_reads_same_strand
 # linear_BSJ_reads_opposite_strand
 # linear_spliced_BSJ_reads_opposite_strand
-localrules:
-    create_circExplorer_merged_found_counts_table,
-
 
 rule create_circExplorer_merged_found_counts_table:
     input:
@@ -404,10 +401,6 @@ else:
     """
 
 
-localrules:
-    merge_alignment_stats,
-
-
 rule merge_alignment_stats:
     input:
         expand(
@@ -432,7 +425,7 @@ for f in {input};do
         paste {output} {params.tmpdir}/${{count}} > {params.tmpdir}/${{count}}.tmp
         mv {params.tmpdir}/${{count}}.tmp {output}
     fi
-done 
+done
 """
 
 
diff --git a/workflow/scripts/Create_circExplorer_BSJ_count_matrix.py b/workflow/scripts/Create_circExplorer_BSJ_count_matrix.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/Create_circExplorer_count_matrix.py b/workflow/scripts/Create_circExplorer_count_matrix.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/Create_ciri_count_matrix.py b/workflow/scripts/Create_ciri_count_matrix.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_add_geneid2genepred.py b/workflow/scripts/_add_geneid2genepred.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_append_splice_site_flanks_to_BSJs.py b/workflow/scripts/_append_splice_site_flanks_to_BSJs.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_bam_filter_BSJ_for_HQonly.py b/workflow/scripts/_bam_filter_BSJ_for_HQonly.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_bam_get_alignment_stats.py b/workflow/scripts/_bam_get_alignment_stats.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_bamtobed2readendsbed.py b/workflow/scripts/_bamtobed2readendsbed.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_bedintersect_to_rid2jid.py b/workflow/scripts/_bedintersect_to_rid2jid.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_bedpe2bed.py b/workflow/scripts/_bedpe2bed.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_circExplorer_BSJ_get_strand.py b/workflow/scripts/_circExplorer_BSJ_get_strand.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_circExplorer_BSJ_get_strand.sh b/workflow/scripts/_circExplorer_BSJ_get_strand.sh
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_collapse_find_circ.py b/workflow/scripts/_collapse_find_circ.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_compare_lists.py b/workflow/scripts/_compare_lists.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_create_circExplorer_BSJ_bam_pe.py b/workflow/scripts/_create_circExplorer_BSJ_bam_pe.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_create_circExplorer_BSJ_bam_se.py b/workflow/scripts/_create_circExplorer_BSJ_bam_se.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_create_circExplorer_BSJ_hqonly_pe.py b/workflow/scripts/_create_circExplorer_BSJ_hqonly_pe.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_create_circExplorer_linear_bam.v2.sh b/workflow/scripts/_create_circExplorer_linear_bam.v2.sh
old mode 100644
new mode 100755
index f415ad9..cf44b03
--- a/workflow/scripts/_create_circExplorer_linear_bam.v2.sh
+++ b/workflow/scripts/_create_circExplorer_linear_bam.v2.sh
@@ -78,10 +78,10 @@ function printtime() {
     start0=$2
     start=$3
     msg=$4
-    end=$(date +%s.%N)    
-    runtime0=$(python -c "print(${end} - ${start0})")
+    end=$(date +%s.%N)
+    runtime0=$(python -E -c "print(${end} - ${start0})")
     runtime0=${runtime0%.*}
-    runtime=$(python -c "print(${end} - ${start})")
+    runtime=$(python -E -c "print(${end} - ${start})")
     runtime=${runtime%.*}
     echo "$scriptname | $runtime0 | $runtime | $msg"
 }
@@ -156,7 +156,7 @@ start=$(date +%s.%N)
 
 bedtools bamtobed -split -i $filtered_bam > ${tmpdir}/${sample_name}.bed
 
-python ${SCRIPT_DIR}/_process_bamtobed.py \
+python -E ${SCRIPT_DIR}/_process_bamtobed.py \
     --inbed ${tmpdir}/${sample_name}.bed \
     --outbed ${tmpdir}/${sample_name}.readends.bed \
     --linear ${tmpdir}/${sample_name}.linear.readids.gz \
diff --git a/workflow/scripts/_extract_circExplorer_linear_reads.py b/workflow/scripts/_extract_circExplorer_linear_reads.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_filter_linear_spliced_readids_w_rid2jid.py b/workflow/scripts/_filter_linear_spliced_readids_w_rid2jid.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_make_master_counts_table.py b/workflow/scripts/_make_master_counts_table.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_make_merge_per_sample_sh.py b/workflow/scripts/_make_merge_per_sample_sh.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_merge_circExplorer_found_counts.py b/workflow/scripts/_merge_circExplorer_found_counts.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_merge_per_sample_counts_table.py b/workflow/scripts/_merge_per_sample_counts_table.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_multifasta2separatefastas.sh b/workflow/scripts/_multifasta2separatefastas.sh
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_process_bamtobed.py b/workflow/scripts/_process_bamtobed.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/_run_circExplorer_bwa.sh b/workflow/scripts/_run_circExplorer_bwa.sh
old mode 100644
new mode 100755
index 1234ff3..4f7951e
--- a/workflow/scripts/_run_circExplorer_bwa.sh
+++ b/workflow/scripts/_run_circExplorer_bwa.sh
@@ -63,12 +63,12 @@ cat back_spliced_junction.filter1.bed|tr '/' '\t'|cut -f1-3,5- |awk -v m=$MINREA
 # 1. both chromosomes are the same
 # 2. both strands are the same
 # 3. both coordinates are NOT the same
-# as the junction file will be empy for BWA .. this strategy needs to be redone!
+# as the junction file will be empty for BWA .. this strategy needs to be redone!
 # awk '$1==$4' junction |awk '$3==$6' | awk '$2!=$5' > junction.filter1
 
-# use junctions file to get the true strand (not + as reported in back_spliced_junction.bed) ... this is done 
+# use junctions file to get the true strand (not + as reported in back_spliced_junction.bed) ... this is done
 # using _circExplorer_BSJ_get_strand.sh ... and replace it to create new BSJ BED
-# while read seq s e score name ostrand;do 
+# while read seq s e score name ostrand;do
 # 	strand=$(bash ${SCRIPTDIR}/_circExplorer_BSJ_get_strand.sh $seq $s $e junction.filter1)
 # 	echo -ne "$seq\t$s\t$e\t$score\t.\t$strand\n"
 # done < back_spliced_junction.filter2.bed > back_spliced_junction.filter2.strand_fixed.bed
@@ -89,7 +89,7 @@ cp low_conf_circRNA_known.txt $LOWCONF
 cat $KNOWNTXT |tr '/' '\t'|cut -f1-3,5- |awk -v m=$MINREADS '$4>=m' > $FILTEREDKNOWNTXT
 cat $LOWCONF |tr '/' '\t'|cut -f1-3,5- |awk -v m=$MINREADS '$4>=m' > $FILTEREDLOWCONF
 
-python ${SCRIPTDIR}/circExplorer_get_annotated_counts_per_sample.py \
+python -E ${SCRIPTDIR}/circExplorer_get_annotated_counts_per_sample.py \
 	--back_spliced_bed $STRANDFIXEDBSJBED \
 	--back_spliced_min_reads $MINREADS \
 	--circularRNA_known $FILTEREDKNOWNTXT \
diff --git a/workflow/scripts/_run_circExplorer_star.sh b/workflow/scripts/_run_circExplorer_star.sh
old mode 100644
new mode 100755
index cd4ac9f..0ecd1fb
--- a/workflow/scripts/_run_circExplorer_star.sh
+++ b/workflow/scripts/_run_circExplorer_star.sh
@@ -56,7 +56,7 @@ CIRCexplorer2 parse -t STAR junction > $PARSELOG 2>&1
 # copy back original back_spliced BED file
 cp back_spliced_junction.bed $ORIGINALBSJBED
 
-python ${SCRIPTDIR}/_circExplorer_BSJ_get_strand.py ${JUNCTIONFILE} back_spliced_junction.bed ${MINREADS} > back_spliced_junction.strand_fixed.bed
+python -E ${SCRIPTDIR}/_circExplorer_BSJ_get_strand.py ${JUNCTIONFILE} back_spliced_junction.bed ${MINREADS} > back_spliced_junction.strand_fixed.bed
 
 # copy back strand_fixed BSJ BED
 cp back_spliced_junction.strand_fixed.bed $STRANDFIXEDBSJBED
@@ -72,7 +72,7 @@ cp low_conf_circRNA_known.txt $LOWCONF
 cat $KNOWNTXT |tr '/' '\t'|cut -f1-3,5- |awk -v m=$MINREADS '$4>=m' > $FILTEREDKNOWNTXT
 cat $LOWCONF |tr '/' '\t'|cut -f1-3,5- |awk -v m=$MINREADS '$4>=m' > $FILTEREDLOWCONF
 
-python ${SCRIPTDIR}/circExplorer_get_annotated_counts_per_sample.py \
+python -E ${SCRIPTDIR}/circExplorer_get_annotated_counts_per_sample.py \
 	--back_spliced_bed $STRANDFIXEDBSJBED \
 	--back_spliced_min_reads $MINREADS \
 	--circularRNA_known $FILTEREDKNOWNTXT \
diff --git a/workflow/scripts/annotate_clear_quant.py b/workflow/scripts/annotate_clear_quant.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/apply_junction_filters.py b/workflow/scripts/apply_junction_filters.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/bam_get_max_readlen.py b/workflow/scripts/bam_get_max_readlen.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/bam_split_by_regions.py b/workflow/scripts/bam_split_by_regions.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/bam_to_bigwig.sh b/workflow/scripts/bam_to_bigwig.sh
old mode 100644
new mode 100755
diff --git a/workflow/scripts/circExplorer_get_annotated_counts_per_sample.py b/workflow/scripts/circExplorer_get_annotated_counts_per_sample.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/create_circExplorer_linear_bam.py b/workflow/scripts/create_circExplorer_linear_bam.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/create_circExplorer_per_sample_counts_table.py b/workflow/scripts/create_circExplorer_per_sample_counts_table.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/create_dcc_per_sample_counts_table.py b/workflow/scripts/create_dcc_per_sample_counts_table.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/create_mapsplice_per_sample_counts_table.py b/workflow/scripts/create_mapsplice_per_sample_counts_table.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/create_nclscan_per_sample_counts_table.py b/workflow/scripts/create_nclscan_per_sample_counts_table.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/filter_bam.py b/workflow/scripts/filter_bam.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/filter_bam_by_readids.py b/workflow/scripts/filter_bam_by_readids.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/filter_bam_for_BSJs.py b/workflow/scripts/filter_bam_for_BSJs.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/filter_bam_for_linear_reads.py b/workflow/scripts/filter_bam_for_linear_reads.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/filter_bam_for_splice_reads.py b/workflow/scripts/filter_bam_for_splice_reads.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/filter_dcc.py b/workflow/scripts/filter_dcc.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/filter_junction.py b/workflow/scripts/filter_junction.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/filter_junction_human.py b/workflow/scripts/filter_junction_human.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/fix_gtfs.py b/workflow/scripts/fix_gtfs.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/fix_refseq_gtf.py b/workflow/scripts/fix_refseq_gtf.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/gather_cluster_stats.sh b/workflow/scripts/gather_cluster_stats.sh
old mode 100644
new mode 100755
diff --git a/workflow/scripts/get_index_rl.py b/workflow/scripts/get_index_rl.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/junctions2readids.py b/workflow/scripts/junctions2readids.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/make_star_index.sh b/workflow/scripts/make_star_index.sh
old mode 100644
new mode 100755
diff --git a/workflow/scripts/merge_ReadsPerGene_counts.R b/workflow/scripts/merge_ReadsPerGene_counts.R
old mode 100644
new mode 100755
diff --git a/workflow/scripts/merge_counts_tables_2_counts_matrix.py b/workflow/scripts/merge_counts_tables_2_counts_matrix.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/reformat_hg38_2_hg19.py b/workflow/scripts/reformat_hg38_2_hg19.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/set_singularity_bind_paths.py b/workflow/scripts/set_singularity_bind_paths.py
new file mode 100755
index 0000000..47d70ba
--- /dev/null
+++ b/workflow/scripts/set_singularity_bind_paths.py
@@ -0,0 +1,111 @@
+#!/usr/bin/env python
+"""
+set_singularity_bind_paths.py <config_filename> <samples_filename>
+"""
+import os
+import pathlib
+import sys
+import yaml
+
+
+def print_bind_paths(config_filename, samples_filename):
+    bind_paths = resolve_additional_bind_paths(
+        get_paths(config_filename, samples_filename)
+    )
+    print(",".join(bind_paths))
+
+
+def get_paths(config_filename, samples_filename):
+    paths = set()
+    with open(config_filename, "r") as config_file:
+        config = yaml.safe_load(config_file)
+    conf_keys = [
+        "workdir",
+        "samples",
+        "nclscan_config",
+        "scriptsdir",
+        "resourcesdir",
+        "cluster",
+        "adapters",
+        "fastas_gtfs_dir",
+    ]
+    # exclude tempdir from bind paths
+    for key in conf_keys:
+        if key in config:
+            paths.add(config[key])
+
+    with open(samples_filename, "r") as samples_file:
+        next(samples_file)  # skip header
+        for line in samples_file:
+            line_spl = line.split("\t")
+            if len(line_spl) > 1:
+                paths.add(line_spl[1])
+            if len(line_spl) > 2:
+                paths.add(line_spl[2])
+
+    return paths
+
+
+def resolve_additional_bind_paths(search_paths):
+    """Adapted from RENEE
+
+    Finds additional singularity bind paths from a list of random paths. Paths are
+    indexed with a compostite key containing the first two directories of an absolute
+    file path to avoid issues related to shared names across the /gpfs shared network
+    filesystem. For each indexed list of file paths, a common path is found. Assumes
+    that the paths provided are absolute paths, the renee build sub command creates
+    resource file index with absolute filenames.
+    @param search_paths list[<str>]:
+        List of absolute file paths to find common bind paths from
+    @return common_paths list[<str>]:
+        Returns a list of common shared file paths to create additional singularity bind paths
+    """
+    common_paths = []
+    indexed_paths = {}
+
+    for ref in search_paths:
+        # Skip over resources with remote URI and
+        # skip over strings that are not file PATHS as
+        # RENEE build creates absolute resource PATHS
+        if (
+            ref.lower().startswith("sftp://")
+            or ref.lower().startswith("s3://")
+            or ref.lower().startswith("gs://")
+            or not ref.lower().startswith(os.sep)
+        ):
+            continue
+
+        # Break up path into directory tokens
+        for r in [
+            ref,
+            str(pathlib.Path(ref).resolve()),
+        ]:  # taking care of paths which are symlinks!
+            path_list = os.path.abspath(r).split(os.sep)
+
+            try:  # Create composite index from first two directories
+                # Avoids issues created by shared /gpfs/ PATHS
+                index = path_list[1:3]
+                index = tuple(index)
+            except IndexError:
+                index = path_list[1]  # ref startswith /
+            if index not in indexed_paths:
+                indexed_paths[index] = []
+            # Create an INDEX to find common PATHS for each root child directory
+            # like /scratch or /data. This prevents issues when trying to find the
+            # common path between these two different directories (resolves to /)
+            indexed_paths[index].append(str(os.sep).join(path_list))
+
+    for index, paths in indexed_paths.items():
+        # Find common paths for each path index
+        common_paths.append(os.path.dirname(os.path.commonprefix(paths)))
+
+    return sorted(set(common_paths))
+
+
+if __name__ == "__main__":
+    if len(sys.argv) < 3:
+        print(__doc__)
+        raise Exception("Please provide two arguments")
+    config_filename = sys.argv[1]
+    samples_filename = sys.argv[2]
+    print_bind_paths(config_filename, samples_filename)
diff --git a/workflow/scripts/transcript2gene.py b/workflow/scripts/transcript2gene.py
old mode 100644
new mode 100755
diff --git a/workflow/scripts/validate_BSJ_reads_and_split_BSJ_bam_by_strand.py b/workflow/scripts/validate_BSJ_reads_and_split_BSJ_bam_by_strand.py
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diff --git a/workflow/scripts/venn.R b/workflow/scripts/venn.R
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