diff --git a/aspen b/aspen
index c767af2..64ae457 100755
--- a/aspen
+++ b/aspen
@@ -40,7 +40,7 @@ EOF
 ##########################################################################################
 
 # ## setting PIPELINE_HOME
-PIPELINE_HOME=$(readlink -f $(dirname "$0"))
+export PIPELINE_HOME=$(readlink -f $(dirname "$0"))
 
 # set snakefile
 SNAKEFILE="${PIPELINE_HOME}/workflow/Snakefile"
@@ -58,10 +58,10 @@ PYTHONVERSION="python/3.10"
 SNAKEMAKEVERSION="snakemake"
 #SINGULARITYVERSION="singularity/3.7.4"
 SINGULARITYVERSION="singularity"
-ASPENVERSION=$(head -n1 $VERSIONFILE|awk '{print $1}')
+export ASPENVERSION=$(head -n1 $VERSIONFILE|awk '{print $1}')
 
 # set defaults
-GENOME="hg38"
+export GENOME="hg38"
 SUPPORTED_GENOMES="hg19 hg38 mm10 mmul10 bosTau9 hs1"
 
 # essential files
@@ -193,9 +193,7 @@ mkdir -p $WORKDIR
 f="${PIPELINE_HOME}/config/config.yaml"
 echo "Copying essential file: $f"
 fbn=$(basename $f)
-sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" \
-  -e "s/WORKDIR/${WORKDIR//\//\\/}/g" \
-  -e "s/GENOME/${GENOME}/g" $f > $WORKDIR/$fbn
+cat $f | envsubst '$PIPELINE_HOME $WORKDIR $GENOME $ASPENVERSION' > $WORKDIR/$fbn
 
 for f in ${PIPELINE_HOME}/resources/cluster.json ${PIPELINE_HOME}/resources/tools.yaml
 do
@@ -215,9 +213,7 @@ if [[ "$MANIFEST_SUPPLIED" == "false" ]];then
 f=$MANIFEST
 echo "Copying essential file: $f"
 fbn=$(basename $f)
-sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" \
-  -e "s/WORKDIR/${WORKDIR//\//\\/}/g" \
-  -e "s/GENOME/${GENOME}/g" $f > $WORKDIR/$fbn
+cat $f | envsubst '$PIPELINE_HOME $WORKDIR $GENOME $ASPENVERSION' > $WORKDIR/$fbn
 fi
 
 # copy essential folders
@@ -296,10 +292,9 @@ function reconfig(){
 # 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" \
-    -e "s/GENOME/${GENOME}/g" \
-    ${PIPELINE_HOME}/config/config.yaml > $WORKDIR/config.yaml
+  cat ${PIPELINE_HOME}/config/config.yaml |\
+    envsubst '$PIPELINE_HOME $WORKDIR $GENOME $ASPENVERSION' \
+    > $WORKDIR/config.yaml
   echo "$WORKDIR/config.yaml has been updated!"
 
 }
@@ -716,7 +711,7 @@ function main(){
         if [ ! -f $MANIFEST ];then err "File $MANIFEST does NOT exist!";fi
       ;;
       -g=*|--genome=*)
-        GENOME="${i#*=}"
+        export GENOME="${i#*=}"
         found=0
         for g in $SUPPORTED_GENOMES;do
           if [[ "$GENOME" == "$g" ]];then
@@ -739,7 +734,7 @@ function main(){
       ;;
   esac
   done
-  WORKDIR=$(readlink -f "$WORKDIR")
+  export WORKDIR=$(readlink -f "$WORKDIR")
   MANIFEST_SUPPLIED="true"
   # if manifest is empty ... aka not supplied at cli
   if [[ -z $MANIFEST ]];then
diff --git a/config/config.yaml b/config/config.yaml
index 153c46f..9909372 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -1,20 +1,20 @@
 ## you probably need to change or comment or uncomment some of these
 #
 # The working dir... output will be in the results subfolder of the workdir
-workdir: "WORKDIR"
+workdir: "$WORKDIR"
 
 # tools scriptsdir resourcesdir
 # to use the workdir version of tools.yaml comment out the following line
-tools: "PIPELINE_HOME/resources/tools.yaml"
+tools: "$PIPELINE_HOME/resources/tools.yaml"
 
 # to use the workdir version of cluster.json comment out the following line
-# clusterjson: "PIPELINE_HOME/resources/cluster.json"
+# clusterjson: "$PIPELINE_HOME/resources/cluster.json"
 
 # to use the workdir version of scriptsdir comment out the following line
-# scriptsdir: "PIPELINE_HOME/workflow/scripts"
-scriptsdir: "WORKDIR/scripts"
+# scriptsdir: "$PIPELINE_HOME/workflow/scripts"
+scriptsdir: "$WORKDIR/scripts"
 
-resourcesdir: "PIPELINE_HOME/resources"
+resourcesdir: "$PIPELINE_HOME/resources"
 
 # tab delimited samples file ... should have the following 4 columns
 #
@@ -23,10 +23,10 @@ resourcesdir: "PIPELINE_HOME/resources"
 # multiple replicates may belong to the same sample
 # PE data is required!
 #
-samplemanifest: "WORKDIR/samples.tsv"
+samplemanifest: "$WORKDIR/samples.tsv"
 
 # uncomment the genome of interest
-genome: "GENOME"
+genome: "$GENOME"
 # genome: "hg38"
 # genome: "hg19"
 # genome: "mm10"
@@ -43,7 +43,7 @@ multimapping: 4
 fixed_width: 500
 
 # contrasts info
-contrasts: "WORKDIR/contrasts.tsv"
+contrasts: "$WORKDIR/contrasts.tsv"
 contrasts_fc_cutoff: 2
 contrasts_fdr_cutoff: 0.05
 
@@ -51,71 +51,71 @@ contrasts_fdr_cutoff: 0.05
 
 hs1:
   indexdir: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs1/indexes"
-  blacklistFa: "PIPELINE_HOME/resources/blacklistFa/hs1.blacklist.fa.gz"
-  tssBed: "PIPELINE_HOME/resources/tssBed/hs1_tssbeds.tar.gz"
-  homermotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_mono_homer_format_0.001.motif"
-  mememotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz"
+  blacklistFa: "$PIPELINE_HOME/resources/blacklistFa/hs1.blacklist.fa.gz"
+  tssBed: "$PIPELINE_HOME/resources/tssBed/hs1_tssbeds.tar.gz"
+  homermotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_mono_homer_format_0.001.motif"
+  mememotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz"
   effectiveGenomeSize: 3000000000
   fripextra:
-    dhsbed: "PIPELINE_HOME/resources/frip/hs1.DHS.bed.gz"
-    promoterbed: "PIPELINE_HOME/resources/frip/hs1.promoters.bed.gz"
-    enhancerbed: "PIPELINE_HOME/resources/frip/hs1.enhancers.bed.gz"
+    dhsbed: "$PIPELINE_HOME/resources/frip/hs1.DHS.bed.gz"
+    promoterbed: "$PIPELINE_HOME/resources/frip/hs1.promoters.bed.gz"
+    enhancerbed: "$PIPELINE_HOME/resources/frip/hs1.enhancers.bed.gz"
 
 hg38:
   indexdir: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/indexes"
-  blacklistFa: "PIPELINE_HOME/resources/blacklistFa/hg38.blacklist.fa.gz"
-  tssBed: "PIPELINE_HOME/resources/tssBed/hg38_tssbeds.tar.gz"
-  homermotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_mono_homer_format_0.001.motif"
-  mememotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz"
+  blacklistFa: "$PIPELINE_HOME/resources/blacklistFa/hg38.blacklist.fa.gz"
+  tssBed: "$PIPELINE_HOME/resources/tssBed/hg38_tssbeds.tar.gz"
+  homermotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_mono_homer_format_0.001.motif"
+  mememotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz"
   effectiveGenomeSize: 2700000000
   fripextra:
-    dhsbed: "PIPELINE_HOME/resources/frip/hg38.DHS.bed.gz"
-    promoterbed: "PIPELINE_HOME/resources/frip/hg38.promoters.bed.gz"
-    enhancerbed: "PIPELINE_HOME/resources/frip/hg38.enhancers.bed.gz"
+    dhsbed: "$PIPELINE_HOME/resources/frip/hg38.DHS.bed.gz"
+    promoterbed: "$PIPELINE_HOME/resources/frip/hg38.promoters.bed.gz"
+    enhancerbed: "$PIPELINE_HOME/resources/frip/hg38.enhancers.bed.gz"
 
 hg19:
   indexdir: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_basic/indexes"
-  blacklistFa: "PIPELINE_HOME/resources/blacklistFa/hg19.blacklist.fa.gz"
-  tssBed: "PIPELINE_HOME/resources/tssBed/hg19_tssbeds.tar.gz"
-  homermotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_mono_homer_format_0.001.motif"
-  mememotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz"
+  blacklistFa: "$PIPELINE_HOME/resources/blacklistFa/hg19.blacklist.fa.gz"
+  tssBed: "$PIPELINE_HOME/resources/tssBed/hg19_tssbeds.tar.gz"
+  homermotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_mono_homer_format_0.001.motif"
+  mememotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz"
   effectiveGenomeSize: 2700000000
   fripextra:
-    dhsbed: "PIPELINE_HOME/resources/frip/hg19.DHS.bed.gz"
-    promoterbed: "PIPELINE_HOME/resources/frip/hg19.promoters.bed.gz"
-    enhancerbed: "PIPELINE_HOME/resources/frip/hg19.enhancers.bed.gz"
+    dhsbed: "$PIPELINE_HOME/resources/frip/hg19.DHS.bed.gz"
+    promoterbed: "$PIPELINE_HOME/resources/frip/hg19.promoters.bed.gz"
+    enhancerbed: "$PIPELINE_HOME/resources/frip/hg19.enhancers.bed.gz"
 
 mm10:
   indexdir: "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes"
-  blacklistFa: "PIPELINE_HOME/resources/blacklistFa/mm10.blacklist.fa.gz"
-  tssBed: "PIPELINE_HOME/resources/tssBed/mm10_tssbeds.tar.gz"
-  homermotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_MOUSE_mono_homer_format_0.001.motif"
-  mememotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_MOUSE_mono_meme_format.tar.gz"
+  blacklistFa: "$PIPELINE_HOME/resources/blacklistFa/mm10.blacklist.fa.gz"
+  tssBed: "$PIPELINE_HOME/resources/tssBed/mm10_tssbeds.tar.gz"
+  homermotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_MOUSE_mono_homer_format_0.001.motif"
+  mememotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_MOUSE_mono_meme_format.tar.gz"
   effectiveGenomeSize: 1870000000
   fripextra:
-    dhsbed: "PIPELINE_HOME/resources/frip/mm10.DHS.bed.gz"
-    promoterbed: "PIPELINE_HOME/resources/frip/mm10.promoters.bed.gz"
-    enhancerbed: "PIPELINE_HOME/resources/frip/mm10.enhancers.bed.gz"
+    dhsbed: "$PIPELINE_HOME/resources/frip/mm10.DHS.bed.gz"
+    promoterbed: "$PIPELINE_HOME/resources/frip/mm10.promoters.bed.gz"
+    enhancerbed: "$PIPELINE_HOME/resources/frip/mm10.enhancers.bed.gz"
 
 mmul10:
   indexdir: "/data/CCBR_Pipeliner/db/PipeDB/Indices/mmul10"
-  blacklistFa: "PIPELINE_HOME/resources/blacklistFa/mmul10.blacklist.fa.gz"
-  tssBed: "PIPELINE_HOME/resources/tssBed/mmul10_v108_tssbeds.tar.gz"
-  homermotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_MOUSE_mono_homer_format_0.001.motif"
-  mememotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_MOUSE_mono_meme_format.tar.gz"
+  blacklistFa: "$PIPELINE_HOME/resources/blacklistFa/mmul10.blacklist.fa.gz"
+  tssBed: "$PIPELINE_HOME/resources/tssBed/mmul10_v108_tssbeds.tar.gz"
+  homermotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_MOUSE_mono_homer_format_0.001.motif"
+  mememotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_MOUSE_mono_meme_format.tar.gz"
   effectiveGenomeSize: 2000000000
   fripextra:
-    promoterbed: "PIPELINE_HOME/resources/frip/mmul10.promoters.bed.gz"
+    promoterbed: "$PIPELINE_HOME/resources/frip/mmul10.promoters.bed.gz"
 
 bosTau9:
   indexdir: "/data/CCBR_Pipeliner/db/PipeDB/Indices/bosTau9"
-  blacklistFa: "PIPELINE_HOME/resources/blacklistFa/bosTau9.blacklist.fa.gz"
-  tssBed: "PIPELINE_HOME/resources/tssBed/bosTau9_v108_tssbeds.tar.gz"
-  homermotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_MOUSE_mono_homer_format_0.001.motif"
-  mememotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_MOUSE_mono_meme_format.tar.gz"
+  blacklistFa: "$PIPELINE_HOME/resources/blacklistFa/bosTau9.blacklist.fa.gz"
+  tssBed: "$PIPELINE_HOME/resources/tssBed/bosTau9_v108_tssbeds.tar.gz"
+  homermotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_MOUSE_mono_homer_format_0.001.motif"
+  mememotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_MOUSE_mono_meme_format.tar.gz"
   effectiveGenomeSize: 2000000000
   fripextra:
-    promoterbed: "PIPELINE_HOME/resources/frip/bosTau9.promoters.bed.gz"
+    promoterbed: "$PIPELINE_HOME/resources/frip/bosTau9.promoters.bed.gz"
 
 # MACS2 arguments/parameters for peak calling
 # annotatePeaks: True ensures annotation of called peaks using ChIPSeeker
@@ -154,13 +154,13 @@ roi_min_spm: 2
 # report customized using multiqc_atacseq_config.yaml
 multiqc:
   extraparams: ""
-  configfile: "PIPELINE_HOME/config/multiqc_atacseq_config.yaml"
+  configfile: "$PIPELINE_HOME/config/multiqc_atacseq_config.yaml"
 
 # set min peaks to use for jaccard calculations
 jaccard_min_peaks: 1000
 
 # fastq screen configuration file
-fastqscreen_config: "PIPELINE_HOME/config/fastq_screen_config.txt"
+fastqscreen_config: "$PIPELINE_HOME/config/fastq_screen_config.txt"
 
 # URLs for containers
 # masterdocker: "docker://nciccbr/ccbr_atacseq:v0.1.29"
@@ -170,3 +170,7 @@ fastqscreendocker: "docker://nciccbr/ccbr_fastq_screen_0.14.1:v1.0"
 # featurecounts: "docker://genomicpariscentre/featurecounts:1.5.3"
 featurecountsdocker: "docker://dsaha0295/featurecounts:latest"
 baser: "docker://nciccbr/ccbr_baser:230531"
+
+# pipeline information
+pipeline: "ASPEN"
+version: "$ASPENVERSION"
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 513c169..d96d546 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -53,38 +53,35 @@ rule all:
         expand(join(RESULTSDIR,"peaks","genrich","{sample}.consensus.genrich.peakfiles"),sample=SAMPLES),
         expand(join(RESULTSDIR,"peaks","genrich","{sample}.replicate.genrich.peakfiles"),sample=SAMPLES),
         expand(join(RESULTSDIR,"peaks","genrich","{sample}.genrich.tn5nicksbedfiles"),sample=SAMPLES),
-        # roi gtf 
+        # roi gtf
         expand(join(RESULTSDIR,"peaks","{peakcaller}","fixed_width","ROI.gtf"),peakcaller=PEAKCALLERS),
         # counts matrix
         expand(join(RESULTSDIR,"peaks","{peakcaller}","ROI.counts.tsv"),peakcaller=PEAKCALLERS),
         # diffatac
         expand(join(RESULTSDIR, "peaks", "{peakcaller}", "DiffATAC", "all_diff_atacs.tsv"),peakcaller=PEAKCALLERS) if CONTRASTS.shape[0] > 0 else [],
 
-
-# create jobby tables
-jobby_cmd = 'run_jobby_on_snakemake_log snakemake.log | tee logs/snakemake.log.jobby | cut -f2,3,18 > logs/snakemake.log.jobby.short'
-spook_cmd = f'spooker {WORKDIR} ASPEN'
+on_complete = f"""
+for cmd in spooker run_jobby_on_snakemake_log; do
+    if ! command -v $cmd 2>&1 >/dev/null; then
+        export PATH="$PATH:{config['ccbr_tools_path']}"
+    fi
+done
+run_jobby_on_snakemake_log logs/snakemake.log | tee logs/snakemake.log.jobby | cut -f2,3,18 > logs/snakemake.log.jobby.short
+spooker {WORKDIR} {config['pipeline']} {config['version']}
+"""
 
 onsuccess:
     #subprocess.run(shlex.split(jobby_cmd),capture_output=False,shell=False,text=True)
     print("OnSuccess")
     shell("printenv")
     shell("module list")
-    print(jobby_cmd)
-    print("The above command may fail if run_jobby_on_snakemake_log is not in PATH!")
-    shell(jobby_cmd)
-    print(spook_cmd)
-    shell(spook_cmd)
-    print("The above command may fail if spooker is not in PATH or not running on BIOWULF/FRCE!")
+    print(on_complete)
+    shell(on_complete)
 
 onerror:
     #subprocess.run(shlex.split(jobby_cmd),capture_output=False,shell=False,text=True)
     print("OnError")
     shell("printenv")
     shell("module list")
-    print(jobby_cmd)
-    shell(jobby_cmd)
-    print("The above command may fail if run_jobby_on_snakemake_log is not in PATH!")
-    print(spook_cmd)
-    shell(spook_cmd)
-    print("The above command may fail if spooker is not in PATH or not running on BIOWULF/FRCE!")
+    print(on_complete)
+    shell(on_complete)