diff --git a/openbis_all/source/bash/bis-down.sh b/openbis_all/source/bash/bis-down.sh
index fd64d02105111dbf6556235e08ac007679662067..077390461d380d0eb8395a85b4239d9f287b2844 100755
--- a/openbis_all/source/bash/bis-down.sh
+++ b/openbis_all/source/bash/bis-down.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # Shuts down openBIS server
 
-~openbis/sprint/openBIS-server/apache-tomcat/bin/shutdown.sh
+~openbis/sprint/openBIS-server/jetty/bin/shutdown.sh
diff --git a/openbis_all/source/bash/bis-log.sh b/openbis_all/source/bash/bis-log.sh
index 02f36490c504381a482db18cd1e2c0209f4eb2e3..40e78038e3e8ed8129f8233984fde4569a581e7c 100755
--- a/openbis_all/source/bash/bis-log.sh
+++ b/openbis_all/source/bash/bis-log.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # Shows openBIS server log
 
-less ~openbis/sprint/openBIS-server/apache-tomcat/logs/openbis_log.txt
+less ~openbis/sprint/openBIS-server/jetty/logs/openbis_log.txt
diff --git a/openbis_all/source/bash/bis-up.sh b/openbis_all/source/bash/bis-up.sh
index 36602c88e81639aa7ae8895092239eab11198559..fd4c61b5dc82d379c65d7cb3b2473948bdbd29d3 100755
--- a/openbis_all/source/bash/bis-up.sh
+++ b/openbis_all/source/bash/bis-up.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # Starts up openBIS server
 
-~openbis/sprint/openBIS-server/apache-tomcat/bin/startup.sh
+~openbis/sprint/openBIS-server/jetty/bin/startup.sh
diff --git a/openbis_all/source/bash/bis-watch-log.sh b/openbis_all/source/bash/bis-watch-log.sh
index 4e5e104b195e427178a3e30bd1b19927edc68975..53140c1ed97e146821363eff4e9ce04a6ad5b32b 100644
--- a/openbis_all/source/bash/bis-watch-log.sh
+++ b/openbis_all/source/bash/bis-watch-log.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # Shows openBIS server log with tail -f
 
-tail -f ~openbis/sprint/openBIS-server/apache-tomcat/logs/openbis_log.txt
+tail -f ~openbis/sprint/openBIS-server/jetty/logs/openbis_log.txt
diff --git a/openbis_all/source/bash/create_snapshot_openbis_repos.sh b/openbis_all/source/bash/create_snapshot_openbis_repos.sh
index 8ca4dac901cafa0a1a8d5bde826900532672d97a..a01fb2e5ece0bf40de0b255271fae1a057e975f9 100755
--- a/openbis_all/source/bash/create_snapshot_openbis_repos.sh
+++ b/openbis_all/source/bash/create_snapshot_openbis_repos.sh
@@ -36,7 +36,7 @@ TMPDIR="$TMPROOT/$NAME"
 mkdir "$TMPDIR"
 
 # Shutdown servers
-$BASE_DIR/openBIS-server/apache-tomcat/bin/shutdown.sh
+$BASE_DIR/openBIS-server/jetty/bin/shutdown.sh
 $BASE_DIR/datastore_server/datastore_server.sh stop
 
 # Prepare snaphot
@@ -53,7 +53,7 @@ if [ $? -ne 0 ]; then
   rm -fR "$TMPROOT"
   exit 1
 fi
-gtar cf "$TMPDIR/lucene_indices.tar" -C $BASE_DIR/openBIS-server/apache-tomcat indices
+gtar cf "$TMPDIR/lucene_indices.tar" -C $BASE_DIR/openBIS-server/jetty indices
 if [ $? -ne 0 ]; then
   echo "Error tarring lucene indices! (No snapshot created)"
   rm -fR "$TMPROOT"
@@ -61,7 +61,7 @@ if [ $? -ne 0 ]; then
 fi
 
 # Startup servers
-$BASE_DIR/openBIS-server/apache-tomcat/bin/startup.sh
+$BASE_DIR/openBIS-server/jetty/bin/startup.sh
 $BASE_DIR/datastore_server/datastore_server.sh start
 
 # Package snapshot
diff --git a/openbis_all/source/bash/delete_openbis_repos.sh b/openbis_all/source/bash/delete_openbis_repos.sh
index 1562ed79acfab5bc10359f6bd574fa35a69f1c4c..46434b9ee63edba7464e33d25dcdb4f545bf800e 100755
--- a/openbis_all/source/bash/delete_openbis_repos.sh
+++ b/openbis_all/source/bash/delete_openbis_repos.sh
@@ -32,16 +32,16 @@ echo "Creating SnapShot in /tmp with the TAG DELETED_OPENBIS"
 popd
 
 # Shutdown servers
-~/sprint/openBIS-server/apache-tomcat/bin/shutdown.sh
+~/sprint/openBIS-server/jetty/bin/shutdown.sh
 ~/sprint/datastore_server/datastore_server.sh stop
 
 # Remove the repos data
 rm -fR  ~/sprint/datastore_server/data/store/*
 psql -U postgres -c "drop database openbis_productive"
-rm -fR ~/sprint/openBIS-server/apache-tomcat/indices/*
+rm -fR ~/sprint/openBIS-server/jetty/indices/*
 
 # Startup servers (will rebuild the database)
-~/sprint/openBIS-server/apache-tomcat/bin/startup.sh
+~/sprint/openBIS-server/jetty/bin/startup.sh
 
 echo ""
 echo "You need to login to openBIS now and to create the first user with system role"
diff --git a/openbis_all/source/bash/gather_stats.sh b/openbis_all/source/bash/gather_stats.sh
index e0a45bde15b3b60f749fbe80053a898f76e2071c..6be3b552d41768dc100311174a88eb161335a46e 100644
--- a/openbis_all/source/bash/gather_stats.sh
+++ b/openbis_all/source/bash/gather_stats.sh
@@ -29,8 +29,8 @@ SQL="WITH RECURSIVE data_set_parents(id, parent_ids, cycle) AS (
 SELECT count(*) AS cycles FROM data_set_parents WHERE cycle = true;"
 
 SQL_QUERY="psql -c \"$SQL\" openbis_productive"
-JAVA_MAX_HEAP_SIZE="echo -n JAVA_MAX_HEAP_SIZE: ;cat ~openbis/sprint/openBIS-server/apache-tomcat/etc/openbis.conf | grep JAVA_MEM_OPTS | cut -d \- -f 2"
-JAVA_INIT_HEAP_SIZE="echo -n JAVA_INIT_HEAP_SIZE: ;cat ~openbis/sprint/openBIS-server/apache-tomcat/etc/openbis.conf | grep JAVA_MEM_OPTS | cut -d \- -f 3"
+JAVA_MAX_HEAP_SIZE="echo -n JAVA_MAX_HEAP_SIZE: ;cat ~openbis/sprint/openBIS-server/jetty/bin/openbis.conf | grep JAVA_MEM_OPTS | cut -d \- -f 2"
+JAVA_INIT_HEAP_SIZE="echo -n JAVA_INIT_HEAP_SIZE: ;cat ~openbis/sprint/openBIS-server/jetty/bin/openbis.conf | grep JAVA_MEM_OPTS | cut -d \- -f 3"
 JAVA_VERSION="java -version"
 PSQL_VERSION="psql --version | grep PostgreSQL"
 OPENBIS_VERSION="ls -1d ~openbis/sprint-* | cut -d - -f2"
diff --git a/openbis_all/source/bash/has-config-changed.sh b/openbis_all/source/bash/has-config-changed.sh
index 044483f498e9813bb2958d46b2d2a1a894c5583f..4b4b6dd16d4d0c0c4c24d6e9a85ec448d60762a2 100755
--- a/openbis_all/source/bash/has-config-changed.sh
+++ b/openbis_all/source/bash/has-config-changed.sh
@@ -26,12 +26,13 @@ function compare_configs {
 }
 
 compare_configs $CONFIG_DIR/datastore_server-service.properties ~/sprint/datastore_server/etc/service.properties
-TOMCAT_DIR=~/sprint/openBIS-server/apache-tomcat
-compare_configs $CONFIG_DIR/service.properties $TOMCAT_DIR/webapps/openbis/WEB-INF/classes/service.properties
-compare_configs $CONFIG_DIR/openbis.conf $TOMCAT_DIR/etc/openbis.conf
-compare_configs $CONFIG_DIR/images/ $TOMCAT_DIR/webapps/openbis/images/
-compare_configs $CONFIG_DIR/loginHeader.html $TOMCAT_DIR/webapps/openbis/loginHeader.html
-compare_configs $CONFIG_DIR/help.html $TOMCAT_DIR/webapps/openbis/help.html
+SERVER_DIR=~/sprint/openBIS-server/jetty
+WEBAPP_DIR=$SERVER_DIR/work/openbis/webapp
+compare_configs $CONFIG_DIR/service.properties $WEBAPP_DIR/WEB-INF/classes/service.properties
+compare_configs $CONFIG_DIR/openbis.conf $SERVER_DIR/bin/openbis.conf
+compare_configs $CONFIG_DIR/images/ $WEBAPP_DIR/images/
+compare_configs $CONFIG_DIR/loginHeader.html $WEBAPP_DIR/loginHeader.html
+compare_configs $CONFIG_DIR/help.html $WEBAPP_DIR/help.html
 
 
 rm  .dss_changed
diff --git a/openbis_all/source/bash/restore_snapshot_openbis_repos.sh b/openbis_all/source/bash/restore_snapshot_openbis_repos.sh
index 9964d1f4707cde29918a2fd27962fd3804aee810..ff0a68956d8a6368aa2bb98e3201d97d0e633a8c 100755
--- a/openbis_all/source/bash/restore_snapshot_openbis_repos.sh
+++ b/openbis_all/source/bash/restore_snapshot_openbis_repos.sh
@@ -80,11 +80,11 @@ if [ $? -ne 0 ]; then
 fi
 
 # Shutdown servers
-$BASE_DIR/openBIS-server/apache-tomcat/bin/shutdown.sh
+$BASE_DIR/openBIS-server/jetty/bin/shutdown.sh
 $BASE_DIR/datastore_server/datastore_server.sh stop
 
 # Remove the repos data
-rm -fR $BASE_DIR/openBIS-server/apache-tomcat/indices/*
+rm -fR $BASE_DIR/openBIS-server/jetty/indices/*
 if [ $? -ne 0 ]; then
   echo "Error deleting lucene indices (inconsistent state)"
   rm -fR "$TMPROOT"
@@ -120,7 +120,7 @@ if [ $? -ne 0 ]; then
   rm -fR "$TMPROOT"
   exit 1
 fi
-gtar xf "$TMPDIR/lucene_indices.tar" -C $BASE_DIR/openBIS-server/apache-tomcat
+gtar xf "$TMPDIR/lucene_indices.tar" -C $BASE_DIR/openBIS-server/jetty
 if [ $? -ne 0 ]; then
   echo "Error restoring lucene indices (inconsistent state)"
   rm -fR "$TMPROOT"
@@ -128,7 +128,7 @@ if [ $? -ne 0 ]; then
 fi
 
 # Startup servers
-$BASE_DIR/openBIS-server/apache-tomcat/bin/startup.sh
+$BASE_DIR/openBIS-server/jetty/bin/startup.sh
 $BASE_DIR/datastore_server/datastore_server.sh start
 
 # Clean up
diff --git a/openbis_all/source/bash/rsync_logs.sh b/openbis_all/source/bash/rsync_logs.sh
index b9a501b40a06fae2e88ddeafa5c0bb8a92313d64..f75a0275387f6cb646d41544992fc3a182d2d8f7 100644
--- a/openbis_all/source/bash/rsync_logs.sh
+++ b/openbis_all/source/bash/rsync_logs.sh
@@ -1,15 +1,15 @@
 #!/bin/bash
 # saves the auth and usage logs of openBIS and DSS logs
 
-export TOMCAT_LOGS=~openbis/sprint/openBIS-server/apache-tomcat/logs
+export AS_LOGS=~openbis/sprint/openBIS-server/jetty/logs
 export DSS_LOGS=~openbis/sprint/datastore_server/log
 export RSYNC=/usr/bin/rsync
 export DESTINATION=~openbis/logs
 
 [ -d $DESTINATION ] || mkdir -p $DESTINATION
 
-$RSYNC -av $TOMCAT_LOGS/*auth* $DESTINATION
-$RSYNC -av $TOMCAT_LOGS/*usage* $DESTINATION
+$RSYNC -av $AS_LOGS/*auth* $DESTINATION
+$RSYNC -av $AS_LOGS/*usage* $DESTINATION
 $RSYNC -av $DSS_LOGS/* $DESTINATION
 
 if [ -f $DESTINATION/check_logins.sh ]; then
diff --git a/openbis_all/source/bash/sprint_install.sh b/openbis_all/source/bash/sprint_install.sh
index 89bcb29bb5cf65aa1f9abd5c4e0eded2523564ed..c5056f461efebe8a2750e5127ef4d58d203749ef 100755
--- a/openbis_all/source/bash/sprint_install.sh
+++ b/openbis_all/source/bash/sprint_install.sh
@@ -14,7 +14,7 @@ VER=SNAPSHOT
 DATE=`/bin/date +%Y-%m-%d_%H%M`
 DB_NAME=openbis_productive
 DB_SNAPSHOT=~openbis/db_backups
-TOMCAT_DIR=~openbis/sprint/openBIS-server/apache-tomcat
+SERVER_DIR=~openbis/sprint/openBIS-server/jetty
 DAYS_TO_RETAIN=35
 
 if [ $1 ]; then
@@ -38,7 +38,7 @@ alias rm='rm'
 
 if [ -e $SERVERS_PREV_VER ]; then
         echo Stopping the components...
-        ./$SERVERS_PREV_VER/openBIS-server/apache-tomcat/bin/shutdown.sh
+        ./$SERVERS_PREV_VER/openBIS-server/jetty/bin/shutdown.sh
         ./$SERVERS_PREV_VER/datastore_server/datastore_server.sh stop
 fi
 
@@ -59,15 +59,14 @@ ln -s $SERVERS_VER $SERVERS_DIR_ALIAS
 cd $SERVERS_DIR_ALIAS
 unzip -q ../openBIS-server*$VER*
 cd openBIS-server
-./install.sh --nostartup $PWD $CONFIG_DIR/service.properties $CONFIG_DIR/openbis.conf
+./install.sh $PWD $CONFIG_DIR/service.properties $CONFIG_DIR/openbis.conf
 if [ -f $KEYSTORE ]; then
-  cp -p $KEYSTORE apache-tomcat/openBIS.keystore
-  sed 's/-Djavax.net.ssl.trustStore=openBIS.keystore //g' apache-tomcat/bin/startup.sh > new-startup.sh
-  mv -f new-startup.sh apache-tomcat/bin/startup.sh
-  chmod 744 apache-tomcat/bin/startup.sh
+  cp -p $KEYSTORE jetty/etc/openBIS.keystore
+  sed 's/-Djavax.net.ssl.trustStore=openBIS.keystore //g' jetty/bin/openbis.config > new-openbis.config
+  mv -f new-openbis.config jetty/bin/openbis.config
 fi
-cp ~openbis/old/$SERVERS_PREV_VER/openBIS-server/apache-tomcat/conf/server.xml ~openbis/$SERVERS_VER/openBIS-server/apache-tomcat/conf/server.xml
-#apache-tomcat/bin/startup.sh
+cp ~openbis/old/$SERVERS_PREV_VER/openBIS-server/jetty/etc/jetty.xml ~openbis/$SERVERS_VER/openBIS-server/jetty/etc/jetty.xml
+#jetty/bin/startup.sh
 
 echo Installing datastore server...
 cd ..
@@ -89,7 +88,7 @@ cd ~openbis
 mv -f *.zip old/
 rm -rf openbis
 cd ~openbis/sprint/openBIS-server
-rm apache-tomcat.zip install.sh openbis.conf openBIS.keystore openBIS.war passwd.sh server.xml service.properties tomcat-version.txt
+rm jetty.zip install.sh openbis.conf openBIS.keystore openBIS.war passwd.sh jetty.xml service.properties jetty-version.txt
 
 # Reset the rm command alias
 alias 'rm=rm -i'
diff --git a/openbis_all/source/bash/sprint_post_install.sh b/openbis_all/source/bash/sprint_post_install.sh
index ad18644db209a03b1c2c2caf6bc24375017dee9b..58b93a4fe8ae2ebc8b7d343d77e1e122a6e106e3 100755
--- a/openbis_all/source/bash/sprint_post_install.sh
+++ b/openbis_all/source/bash/sprint_post_install.sh
@@ -20,7 +20,7 @@ export PLASMIDS=bs-openbis02.ethz.ch
 function create_individual_greeting_message {
 # Creates an individual greeting message
 	if [ -f ~openbis/config/openbis_instance.txt ]; then
-	   export OPENBIS_DICT=~openbis/sprint/openBIS-server/apache-tomcat/webapps/openbis/common-dictionary.js
+	   export OPENBIS_DICT=~openbis/sprint/openBIS-server/jetty/work/openbis/webapp/common-dictionary.js
 	   export SERVER_INSTANCE_NAME=`cat ~openbis/config/openbis_instance.txt`
 	   perl -pe 's/openbis_instance: "",/openbis_instance: "$ENV{SERVER_INSTANCE_NAME}",/' -i $OPENBIS_DICT
 	fi
@@ -29,15 +29,15 @@ function create_individual_greeting_message {
 function restore_common {
   if [ -f ~openbis/config/loginHeader.html ]; then
     echo restoring loginHeader.html...
-    cp -r ~openbis/config/images ~openbis/sprint/openBIS-server/apache-tomcat/webapps/openbis/
-    cp ~openbis/config/loginHeader.html ~openbis/sprint/openBIS-server/apache-tomcat/webapps/openbis/
-    cp ~openbis/config/help.html ~openbis/sprint/openBIS-server/apache-tomcat/webapps/openbis/
+    cp -r ~openbis/config/images ~openbis/sprint/openBIS-server/jetty/work/openbis/webapp/
+    cp ~openbis/config/loginHeader.html ~openbis/sprint/openBIS-server/jetty/webapps/openbis/
+    cp ~openbis/config/help.html ~openbis/sprint/openBIS-server/jetty/work/openbis/webapp/
   fi
   if [ -f ~openbis/config/index.html ]; then
-  	cp ~openbis/config/index.html  ~openbis/sprint/openBIS-server/apache-tomcat/webapps/openbis/
+  	cp ~openbis/config/index.html  ~openbis/sprint/openBIS-server/jetty/work/openbis/webapp/
   fi  
-  if  [ -f ~openbis/config/server.xml ]; then
-  	cp ~openbis/config/server.xml ~openbis/sprint/openBIS-server/apache-tomcat/conf/
+  if  [ -f ~openbis/config/jetty.xml ]; then
+  	cp ~openbis/config/jetty.xml ~openbis/sprint/openBIS-server/jetty/etc/
   fi
   if  [ -f ~openbis/config/datastore_log.xml ]; then
   	cp ~openbis/config/datastore_log.xml ~openbis/sprint/datastore_server/etc/log.xml
@@ -95,7 +95,7 @@ case "$SERVER" in
 	echo DSU:$DSU;
 	restore_common
 	create_individual_greeting_message
-	DSU_SERVER_HOME=~openbis/sprint/openBIS-server/apache-tomcat-5.5.26/webapps/openbis
+	DSU_SERVER_HOME=~openbis/sprint/openBIS-server/jetty/webapps/openbis
     cp ~openbis/config/openBIS_for_DSU.pdf $DSU_SERVER_HOME
 	;;
 	$SCU)
diff --git a/openbis_all/source/bash/sprint_post_install_agronomics.sh b/openbis_all/source/bash/sprint_post_install_agronomics.sh
index c51e51754146cd6e413e9569dd37ea11159d4ba7..3e6a44a8d6b7b3ad97f23f9500ea6cdc0cd71c24 100644
--- a/openbis_all/source/bash/sprint_post_install_agronomics.sh
+++ b/openbis_all/source/bash/sprint_post_install_agronomics.sh
@@ -5,5 +5,5 @@
 MPAF_DIR=/local0/data/dss_incoming/transcriptomics/mpaf
 [ -d $MPAF_DIR ] || mkdir -p $MPAF_DIR
 
-OPENBIS_SERVER_HOME=/localhome/openbis/sprint/openBIS-server/apache-tomcat-5.5.26/webapps/openbis
+OPENBIS_SERVER_HOME=/localhome/openbis/sprint/openBIS-server/jetty/work/openbis/webapp
 cp ~/config/Guide_to_Using_Agron-omics_openBIS.pdf $OPENBIS_SERVER_HOME
\ No newline at end of file
diff --git a/openbis_all/source/bash/usage_stats.sh b/openbis_all/source/bash/usage_stats.sh
index aa9a4c54d0cac35f1b1604063524109ba57dc23f..ca0239d16938603c93733cdaa7fc1559be4eac6c 100644
--- a/openbis_all/source/bash/usage_stats.sh
+++ b/openbis_all/source/bash/usage_stats.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # Shows openBIS server usage statistics done by users outside CISD
 
-cat ~openbis/sprint/openBIS-server/apache-tomcat/logs/*usage_log.txt* | egrep -v "tpylak|brinn|etlserver|kohleman|izabelaa|buczekp|felmer|hclaus|cramakri|baucha|ryanj" | cut -d" " -f1,8,12 | sort | uniq -c
\ No newline at end of file
+cat ~openbis/sprint/openBIS-server/jetty/logs/*usage_log.txt* | egrep -v "tpylak|brinn|etlserver|kohleman|izabelaa|buczekp|felmer|hclaus|cramakri|baucha|ryanj" | cut -d" " -f1,8,12 | sort | uniq -c
\ No newline at end of file