diff --git a/MQ/histoServer/CMakeLists.txt b/MQ/histoServer/CMakeLists.txt
index a338e1bdabd9921475edb9b479c5c85e6c4e6c46..d6c772e21220eea4077867771c9c0de5bb05a19a 100644
--- a/MQ/histoServer/CMakeLists.txt
+++ b/MQ/histoServer/CMakeLists.txt
@@ -62,6 +62,11 @@ set(DEPENDENCIES_ALL
   ${BOOST_LIBS}
 )
 
+# Set the install path within the build directory
+set(EXECUTABLE_OUTPUT_PATH "${EXECUTABLE_OUTPUT_PATH}/MQ/histogramServer")
+# Set the install path within the installation directory
+set(BIN_DESTINATION bin/MQ/histogramServer)
+
 set(EXE_NAME HistoServer)
 set(SRCS CbmHistoServer.cxx runCbmHistoServer.cxx)
 set(DEPENDENCIES
@@ -76,8 +81,6 @@ set(DEPENDENCIES
 )
 GENERATE_EXECUTABLE()
 
-set(EXECUTABLE_OUTPUT_PATH "${EXECUTABLE_OUTPUT_PATH}/MQ/histogramServer")
-
 set(EXE_NAME MqHistoServer)
 set(SRCS CbmMqHistoServer.cxx runCbmMqHistoServer.cxx)
 set(DEPENDENCIES
diff --git a/MQ/hitbuilder/CMakeLists.txt b/MQ/hitbuilder/CMakeLists.txt
index ba1bdaecb05c9aa56e713422828071033b16712d..44fcefaedf242a5f1713a62cd582888ae247e4b1 100644
--- a/MQ/hitbuilder/CMakeLists.txt
+++ b/MQ/hitbuilder/CMakeLists.txt
@@ -1,5 +1,4 @@
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/startMQSamplerUnpackerParserverHitBuilder.sh.in ${CMAKE_BINARY_DIR}/bin/MQ/topologies/startMQSamplerUnpackerParserverHitBuilder.sh)
-
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/startMQ_Mcbm.sh.in ${CMAKE_BINARY_DIR}/bin/MQ/topologies/startMQ_Mcbm.sh)
 
 set(INCLUDE_DIRECTORIES
@@ -38,7 +37,10 @@ set(LINK_DIRECTORIES
 
 link_directories(${LINK_DIRECTORIES})
 
+# Set the install path within the build directory
 set(EXECUTABLE_OUTPUT_PATH "${EXECUTABLE_OUTPUT_PATH}/MQ/hitbuilder")
+# Set the install path within the installation directory
+set(BIN_DESTINATION bin/MQ/hitbuilder)
 
 Set(BOOST_LIBS
   ${Boost_SYSTEM_LIBRARY}
@@ -86,3 +88,21 @@ set(DEPENDENCIES
 )
 GENERATE_EXECUTABLE()
 
+# Set the correct variables for the installation
+set(VMCWORKDIR ${CMAKE_INSTALL_PREFIX}/share/cbmroot)
+
+set(MY_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+set(CMAKE_CURRENT_SOURCE_DIR ${VMCWORKDIR}/input)
+
+set(TMPDIR "${CMAKE_BINARY_DIR}")
+set(CMAKE_BINARY_DIR ${CMAKE_INSTALL_PREFIX})
+
+# Configure file for installation directory
+configure_file(${MY_SOURCE_DIR}/startMQSamplerUnpackerParserverHitBuilder.sh.in ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerUnpackerParserverHitBuilder.sh)
+configure_file(${MY_SOURCE_DIR}/startMQ_Mcbm.sh.in                      ${TMPDIR}/bin/MQ/topologies/install/startMQ_Mcbm.sh)
+
+install(PROGRAMS ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerUnpackerParserverHitBuilder.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startMQ_Mcbm.sh
+        DESTINATION ${CMAKE_INSTALL_PREFIX}/bin/MQ/topologies
+       )
+
diff --git a/MQ/mcbm/CMakeLists.txt b/MQ/mcbm/CMakeLists.txt
index adf84ff5a753def5503217fe0a8775672e867edc..5df7e0fb21804eeab02cae5ecedc28a2b4137fbd 100644
--- a/MQ/mcbm/CMakeLists.txt
+++ b/MQ/mcbm/CMakeLists.txt
@@ -74,7 +74,10 @@ set(LINK_DIRECTORIES
 
 link_directories(${LINK_DIRECTORIES})
 
+# Set the install path within the build directory
 set(EXECUTABLE_OUTPUT_PATH "${EXECUTABLE_OUTPUT_PATH}/MQ/mcbm")
+# Set the install path within the installation directory
+set(BIN_DESTINATION bin/MQ/mcbm)
 
 Set(BOOST_LIBS
   ${Boost_SYSTEM_LIBRARY}
@@ -115,7 +118,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 set(EXE_NAME McbmMonitorPulser)
@@ -136,7 +138,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 set(EXE_NAME BuildRawEvents)
@@ -163,7 +164,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 
@@ -185,7 +185,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 set(EXE_NAME McbmEventSink)
@@ -207,7 +206,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 
@@ -311,7 +309,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 if (${CMAKE_CXX_STANDARD} EQUAL 17)
@@ -337,3 +334,28 @@ if (${CMAKE_CXX_STANDARD} EQUAL 17)
   GENERATE_EXECUTABLE()
 endif()
 
+# Set the correct variables for the installation
+set(VMCWORKDIR ${CMAKE_INSTALL_PREFIX}/share/cbmroot)
+
+set(MY_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+set(CMAKE_CURRENT_SOURCE_DIR ${VMCWORKDIR}/input)
+
+set(TMPDIR "${CMAKE_BINARY_DIR}")
+set(CMAKE_BINARY_DIR ${CMAKE_INSTALL_PREFIX})
+
+# Configure file for installation directory
+configure_file(${MY_SOURCE_DIR}/startMQMcbmPulserMonitor2020.sh.in   ${TMPDIR}/bin/MQ/topologies/install/startMQMcbmPulserMonitor2020.sh)
+configure_file(${MY_SOURCE_DIR}/startMQMcbmEvtBuilderWin2020.sh.in   ${TMPDIR}/bin/MQ/topologies/install/startMQMcbmEvtBuilderWin2020.sh)
+configure_file(${MY_SOURCE_DIR}/startMQBuildRawEvents.sh.in          ${TMPDIR}/bin/MQ/topologies/install/startMQBuildRawEvents.sh)
+configure_file(${MY_SOURCE_DIR}/startBuildRawEvents2021.sh.in        ${TMPDIR}/bin/MQ/topologies/install/startBuildRawEvents2021.sh)
+configure_file(${MY_SOURCE_DIR}/startBuildRawEventsCosmics2021.sh.in ${TMPDIR}/bin/MQ/topologies/install/startBuildRawEventsCosmics2021.sh)
+configure_file(${MY_SOURCE_DIR}/startEventBuilder.sh.in              ${TMPDIR}/bin/MQ/topologies/startEventBuilder.sh)
+
+install(PROGRAMS ${TMPDIR}/bin/MQ/topologies/install/startMQMcbmPulserMonitor2020.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startMQMcbmEvtBuilderWin2020.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startMQBuildRawEvents.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startBuildRawEvents2021.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startBuildRawEventsCosmics2021.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startEventBuilder.sh
+        DESTINATION ${CMAKE_INSTALL_PREFIX}/bin/MQ/topologies
+       )
diff --git a/MQ/monitor/CMakeLists.txt b/MQ/monitor/CMakeLists.txt
index dd39732bd38ed926759d8d01f9cb6ec503de8076..43c45b98a2574d3f47c17abf7d5e84c539144651 100644
--- a/MQ/monitor/CMakeLists.txt
+++ b/MQ/monitor/CMakeLists.txt
@@ -47,7 +47,10 @@ set(LINK_DIRECTORIES
 
 link_directories(${LINK_DIRECTORIES})
 
+# Set the install path within the build directory
 set(EXECUTABLE_OUTPUT_PATH "${EXECUTABLE_OUTPUT_PATH}/MQ/monitor")
+# Set the install path within the installation directory
+set(BIN_DESTINATION bin/MQ/monitor)
 
 Set(BOOST_LIBS
   ${Boost_SYSTEM_LIBRARY}
@@ -90,7 +93,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 set(EXE_NAME TofMonitorMcbm2018)
@@ -111,7 +113,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 set(EXE_NAME T0MonitorReqMcbm)
@@ -132,7 +133,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 set(EXE_NAME TofMonitorReqMcbm)
@@ -153,7 +153,6 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
 set(EXE_NAME PsdMonitorMcbm2018)
@@ -174,6 +173,37 @@ set(DEPENDENCIES
   Hist
   RHTTP
 )
-#GENERATE_LIBRARY()
 GENERATE_EXECUTABLE()
 
+# Install scripts and input file
+if(EXISTS ${VMCWORKDIR}/input/tofget4_hd2018.tsa)
+  install(FILES ${VMCWORKDIR}/input/tofget4_hd2018.tsa
+          DESTINATION ${CMAKE_INSTALL_PREFIX}/share/cbmroot/input
+         )
+endif()
+
+# Set the correct variables for the installation
+set(VMCWORKDIR ${CMAKE_INSTALL_PREFIX}/share/cbmroot)
+
+set(MY_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+set(CMAKE_CURRENT_SOURCE_DIR ${VMCWORKDIR}/input)
+
+set(TMPDIR "${CMAKE_BINARY_DIR}")
+set(CMAKE_BINARY_DIR ${CMAKE_INSTALL_PREFIX})
+
+# Configure file for installation directory
+configure_file(${MY_SOURCE_DIR}/startMQSamplerMonitor.sh.in        ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerMonitor.sh)
+configure_file(${MY_SOURCE_DIR}/startMQSamplerT0Monitor2020.sh.in  ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerT0Monitor2020.sh)
+configure_file(${MY_SOURCE_DIR}/startMQSamplerTofMonitor2020.sh.in ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerTofMonitor2020.sh)
+configure_file(${MY_SOURCE_DIR}/startMQSamplerT0Monitor2021.sh.in  ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerT0Monitor2021.sh)
+configure_file(${MY_SOURCE_DIR}/startMQSamplerTofMonitor2021.sh.in ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerTofMonitor2021.sh)
+configure_file(${MY_SOURCE_DIR}/startMQSamplerPsdMonitor2021.sh.in ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerPsdMonitor2021.sh)
+
+install(PROGRAMS ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerMonitor.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerT0Monitor2020.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerTofMonitor2020.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerT0Monitor2021.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerTofMonitor2021.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerPsdMonitor2021.sh
+        DESTINATION ${CMAKE_INSTALL_PREFIX}/bin/MQ/topologies
+       )
diff --git a/MQ/parmq/CMakeLists.txt b/MQ/parmq/CMakeLists.txt
index 3f6c9f898862b4bb2a78e862940fc4ccd5264233..299ca939e28c22b6c5703e8114c8beea3b2f3633 100644
--- a/MQ/parmq/CMakeLists.txt
+++ b/MQ/parmq/CMakeLists.txt
@@ -27,7 +27,10 @@ Set(LINK_DIRECTORIES
 
 Link_Directories(${LINK_DIRECTORIES})
 
+# Set the install path within the build directory
 set(EXECUTABLE_OUTPUT_PATH "${EXECUTABLE_OUTPUT_PATH}/MQ/parmq")
+# Set the install path within the installation directory
+set(BIN_DESTINATION bin/MQ/parmq)
 
 Set(BOOST_LIBS
   ${Boost_SYSTEM_LIBRARY}
diff --git a/MQ/sink/CMakeLists.txt b/MQ/sink/CMakeLists.txt
index 0a4294d30f866cd484ba2934abe3444aca1abb4f..731189d3543bf42167379cc674324ddd30177470 100644
--- a/MQ/sink/CMakeLists.txt
+++ b/MQ/sink/CMakeLists.txt
@@ -28,7 +28,10 @@ set(LINK_DIRECTORIES
 
 link_directories(${LINK_DIRECTORIES})
 
+# Set the install path within the build directory
 set(EXECUTABLE_OUTPUT_PATH "${EXECUTABLE_OUTPUT_PATH}/MQ/sink")
+# Set the install path within the installation directory
+set(BIN_DESTINATION bin/MQ/sink)
 
 Set(BOOST_LIBS
   ${Boost_SYSTEM_LIBRARY}
@@ -71,3 +74,25 @@ set(DEPENDENCIES
 )
 GENERATE_EXECUTABLE()
 
+# Install scripts and input file
+if(EXISTS ${VMCWORKDIR}/input/tofget4_hd2018.tsa)
+  install(FILES ${VMCWORKDIR}/input/tofget4_hd2018.tsa
+          DESTINATION ${CMAKE_INSTALL_PREFIX}/share/cbmroot/input
+         )
+endif()
+
+# Set the correct variables for the installation
+set(VMCWORKDIR ${CMAKE_INSTALL_PREFIX}/share/cbmroot)
+
+set(MY_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+set(CMAKE_CURRENT_SOURCE_DIR ${VMCWORKDIR}/input)
+
+set(TMPDIR "${CMAKE_BINARY_DIR}")
+set(CMAKE_BINARY_DIR ${CMAKE_INSTALL_PREFIX})
+
+# Configure file for installation directory
+configure_file(${MY_SOURCE_DIR}/startMQSamplerSink.sh.in ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerSink.sh)
+
+install(PROGRAMS ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerSink.sh
+       DESTINATION ${CMAKE_INSTALL_PREFIX}/bin/MQ/topologies
+       )
diff --git a/MQ/source/CMakeLists.txt b/MQ/source/CMakeLists.txt
index 9b7ee9f90283bebcab13769b5b85d4222412dbaa..3b618ce19dcbc39b8b58703b25bf78e52f7d60e6 100644
--- a/MQ/source/CMakeLists.txt
+++ b/MQ/source/CMakeLists.txt
@@ -42,7 +42,10 @@ set(LINK_DIRECTORIES
 
 link_directories(${LINK_DIRECTORIES})
 
+# Set the install path within the build directory
 set(EXECUTABLE_OUTPUT_PATH "${EXECUTABLE_OUTPUT_PATH}/MQ/source")
+# Set the install path within the installation directory
+set(BIN_DESTINATION bin/MQ/source)
 
 Set(BOOST_LIBS
   ${Boost_SYSTEM_LIBRARY}
@@ -190,3 +193,28 @@ set(DEPENDENCIES
   RIO
 )
 GENERATE_EXECUTABLE()
+
+# Install scripts and input file
+if(EXISTS ${VMCWORKDIR}/input/tofget4_hd2018.tsa)
+  install(FILES ${VMCWORKDIR}/input/tofget4_hd2018.tsa
+          DESTINATION ${CMAKE_INSTALL_PREFIX}/share/cbmroot/input
+         )
+endif()
+
+# Set the correct variables for the installation
+set(VMCWORKDIR ${CMAKE_INSTALL_PREFIX}/share/cbmroot)
+
+set(MY_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+set(CMAKE_CURRENT_SOURCE_DIR ${VMCWORKDIR}/input)
+
+set(TMPDIR "${CMAKE_BINARY_DIR}")
+set(CMAKE_BINARY_DIR ${CMAKE_INSTALL_PREFIX})
+
+# Configure file for installation directory
+configure_file(${MY_SOURCE_DIR}/startMQInfo.sh.in ${TMPDIR}/bin/MQ/topologies/install/startMQInfo.sh)
+configure_file(${MY_SOURCE_DIR}/startMQSampler.sh.in ${TMPDIR}/bin/MQ/topologies/install/startMQSampler.sh)
+
+install(PROGRAMS ${TMPDIR}/bin/MQ/topologies/install/startMQInfo.sh
+                 ${TMPDIR}/bin/MQ/topologies/install/startMQSampler.sh
+        DESTINATION ${CMAKE_INSTALL_PREFIX}/bin/MQ/topologies
+       )
diff --git a/MQ/unpacker/CMakeLists.txt b/MQ/unpacker/CMakeLists.txt
index 7091e5936f640822721dc4f66cb77e4474d8dfb3..0602122e1819afb8a1169f421860df1967898697 100644
--- a/MQ/unpacker/CMakeLists.txt
+++ b/MQ/unpacker/CMakeLists.txt
@@ -83,5 +83,34 @@ set(DEPENDENCIES
   Net
   Hist
 )
+
+# set the install dir
+set(BIN_DESTINATION bin/MQ/unpacker)
 GENERATE_EXECUTABLE()
 
+# Install script and input file(s)
+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/MapTofHdCosmics_v18d.par
+        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/cbmroot/input
+       )
+
+if(EXISTS ${VMCWORKDIR}/input/tofget4_hd2018.tsa)
+  install(FILES ${VMCWORKDIR}/input/tofget4_hd2018.tsa
+          DESTINATION ${CMAKE_INSTALL_PREFIX}/share/cbmroot/input
+         )
+endif()
+
+# Set the correct variables for the installation
+set(VMCWORKDIR ${CMAKE_INSTALL_PREFIX}/share/cbmroot)
+
+set(MY_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+set(CMAKE_CURRENT_SOURCE_DIR ${VMCWORKDIR}/input)
+
+set(TMPDIR "${CMAKE_BINARY_DIR}")
+set(CMAKE_BINARY_DIR ${CMAKE_INSTALL_PREFIX})
+
+# Configure file for installation directory
+configure_file(${MY_SOURCE_DIR}/startMQSamplerUnpackerParserver.sh.in ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerUnpackerParserver.sh)
+
+install(PROGRAMS ${TMPDIR}/bin/MQ/topologies/install/startMQSamplerUnpackerParserver.sh
+        DESTINATION ${CMAKE_INSTALL_PREFIX}/bin/MQ/topologies
+       )