diff --git a/benchmarks/calorimeters/run_emcal_barrel_electrons.sh b/benchmarks/calorimeters/run_emcal_barrel_electrons.sh
index b735f190f2cd8f60cb7d8bac11e80d2440bbbd81..1d284a6942a0f94eddc2b0881c57aae47ff25c81 100755
--- a/benchmarks/calorimeters/run_emcal_barrel_electrons.sh
+++ b/benchmarks/calorimeters/run_emcal_barrel_electrons.sh
@@ -8,9 +8,6 @@ if [[ ! -n  "${JUGGLER_N_EVENTS}" ]] ; then
   export JUGGLER_N_EVENTS=1000
 fi
 
-if [[ ! -n  "${JUGGLER_INSTALL_PREFIX}" ]] ; then 
-  export JUGGLER_INSTALL_PREFIX="/usr/local"
-fi
 
 if [[ ! -n  "${E_start}" ]] ; then
   export E_start=5.0
@@ -30,13 +27,13 @@ echo "JUGGLER_N_EVENTS = ${JUGGLER_N_EVENTS}"
 echo "JUGGLER_DETECTOR = ${JUGGLER_DETECTOR}"
 
 # Generate the input events
-root -b -q "calorimeters/scripts/emcal_barrel_electrons.cxx(${JUGGLER_N_EVENTS}, ${E_start}, ${E_end}, \"${JUGGLER_FILE_NAME_TAG}.hepmc\")"
+root -b -q "benchmarks/calorimeters/scripts/emcal_barrel_electrons.cxx(${JUGGLER_N_EVENTS}, ${E_start}, ${E_end}, \"${JUGGLER_FILE_NAME_TAG}.hepmc\")"
 if [[ "$?" -ne "0" ]] ; then
   echo "ERROR running script: generating input events"
   exit 1
 fi
 # Plot the input events
-root -b -q "calorimeters/scripts/emcal_barrel_electrons_reader.cxx(${E_start}, ${E_end}, \"${JUGGLER_FILE_NAME_TAG}.hepmc\")"
+root -b -q "benchmarks/calorimeters/scripts/emcal_barrel_electrons_reader.cxx(${E_start}, ${E_end}, \"${JUGGLER_FILE_NAME_TAG}.hepmc\")"
 if [[ "$?" -ne "0" ]] ; then
   echo "ERROR running script: plotting input events"
   exit 1
@@ -56,14 +53,6 @@ if [[ "$?" -ne "0" ]] ; then
   exit 1
 fi
 
-# Run Juggler
-xenv -x ${JUGGLER_INSTALL_PREFIX}/Juggler.xenv \
-	gaudirun.py calorimeters/options/emcal_barrel_reco.py
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR running juggler"
-  exit 1
-fi
-
 # Directory for plots
 mkdir -p results
 
diff --git a/benchmarks/calorimeters/run_emcal_barrel_pions.sh b/benchmarks/calorimeters/run_emcal_barrel_pions.sh
index f82bfaa9bc974a5b4207b137d964738f51d311d8..29bbafc4ba94d76292d9fe01d5c98ee40a3e9d17 100755
--- a/benchmarks/calorimeters/run_emcal_barrel_pions.sh
+++ b/benchmarks/calorimeters/run_emcal_barrel_pions.sh
@@ -30,13 +30,13 @@ echo "JUGGLER_N_EVENTS = ${JUGGLER_N_EVENTS}"
 echo "JUGGLER_DETECTOR = ${JUGGLER_DETECTOR}"
 
 # Generate the input events
-root -b -q "calorimeters/scripts/emcal_barrel_pions.cxx(${JUGGLER_N_EVENTS}, ${E_start}, ${E_end}, \"${JUGGLER_FILE_NAME_TAG}.hepmc\")"
+root -b -q "benchmarks/calorimeters/scripts/emcal_barrel_pions.cxx(${JUGGLER_N_EVENTS}, ${E_start}, ${E_end}, \"${JUGGLER_FILE_NAME_TAG}.hepmc\")"
 if [[ "$?" -ne "0" ]] ; then
   echo "ERROR running script: generating input events"
   exit 1
 fi
 # Plot the input events
-root -b -q "calorimeters/scripts/emcal_barrel_pions_reader.cxx(${E_start}, ${E_end}, \"${JUGGLER_FILE_NAME_TAG}.hepmc\")"
+root -b -q "benchmarks/calorimeters/scripts/emcal_barrel_pions_reader.cxx(${E_start}, ${E_end}, \"${JUGGLER_FILE_NAME_TAG}.hepmc\")"
 if [[ "$?" -ne "0" ]] ; then
   echo "ERROR running script: plotting input events"
   exit 1
@@ -56,14 +56,6 @@ if [[ "$?" -ne "0" ]] ; then
   exit 1
 fi
 
-# Run Juggler
-xenv -x ${JUGGLER_INSTALL_PREFIX}/Juggler.xenv \
-        gaudirun.py calorimeters/options/emcal_barrel_reco.py
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR running juggler"
-  exit 1
-fi
-
 # Directory for plots
 mkdir -p results
 
diff --git a/benchmarks/calorimeters/run_simulation_crystal.sh b/benchmarks/calorimeters/run_simulation_crystal.sh
index aabd423092cde1ab27dae07a036c0ad91e2c6bd7..f00e8033bb47611f22c76bed3ba9139a0c9fa44c 100755
--- a/benchmarks/calorimeters/run_simulation_crystal.sh
+++ b/benchmarks/calorimeters/run_simulation_crystal.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
 ddsim --runType batch --numberOfEvents 100 \
-      --compactFile ./calorimeters/Crystal_example.xml \
+      --compactFile benchmarks/calorimeters/Crystal_example.xml \
       --inputFiles  ./data/emcal_electrons.hepmc \
       --outputFile  ./sim_output/output_emcal_electrons.root
diff --git a/benchmarks/calorimeters/run_simulation_crystal_pion.sh b/benchmarks/calorimeters/run_simulation_crystal_pion.sh
index 0d4934ac67366fef120586185182bbbdfe7c1e38..f8eb44f94802cf3b26561788270f6bcdb7166f77 100644
--- a/benchmarks/calorimeters/run_simulation_crystal_pion.sh
+++ b/benchmarks/calorimeters/run_simulation_crystal_pion.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
 npsim --runType batch --numberOfEvents 10000 \
-      --compactFile ./calorimeters/topside.xml \
+      --compactFile benchmarks/calorimeters/topside.xml \
       --inputFiles  ./data/emcal_pions_upto1GeV_10kevents.hepmc \
       --outputFile  ./sim_output/sim_crystal_pion_input.root
diff --git a/benchmarks/calorimeters/run_simulation_zdc.sh b/benchmarks/calorimeters/run_simulation_zdc.sh
index a5d84972b71799021659c7fbb2a3add875b4eb99..6b0744aa99830c3df809a677cca55a7ed4c721af 100755
--- a/benchmarks/calorimeters/run_simulation_zdc.sh
+++ b/benchmarks/calorimeters/run_simulation_zdc.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
 ddsim --runType batch --numberOfEvents 100 \
-      --compactFile ./calorimeters/ZDC_example.xml \
+      --compactFile benchmarks/calorimeters/ZDC_example.xml \
       --inputFiles  ./data/zdc_photons.hepmc \
       --outputFile  ./sim_output/output_zdc_photons.root