diff --git a/.ci/build_compose.sh b/.ci/build_compose.sh
new file mode 100755
index 000000000..5b0150405
--- /dev/null
+++ b/.ci/build_compose.sh
@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+
+set -o errexit
+
+pip --version
+# --user does not work if you are already in a virtual-env
+pip install docker-compose galaxy-parsec --user || pip install docker-compose galaxy-parsec
+
+export DOCKER_RUN_CONTAINER="galaxy-web"
+INSTALL_REPO_ARG="--galaxy-url http://localhost:80"
+SAMPLE_TOOLS=/export/config/sample_tool_list.yaml
+
+pushd $COMPOSE_DIR
+
+# For build script
+export CONTAINER_REGISTRY=quay.io/
+export CONTAINER_USER=bgruening
+./build-orchestration-images.sh --no-push --condor --grafana --slurm --k8s
+
+cat ./tags-for-compose-to-source.sh
+source ./tags-for-compose-to-source.sh
+
+container_size_check   quay.io/bgruening/galaxy-base:$TAG               350 
+container_size_check   quay.io/bgruening/galaxy-web:$TAG                650
+container_size_check   quay.io/bgruening/galaxy-htcondor-base:$TAG      280
+
+export COMPOSE_PROJECT_NAME=galaxy_compose
+docker-compose up -d
+
+until docker-compose exec galaxy-web ps -fC uwsgi
+do
+  echo "sleeping for 20 seconds"
+  sleep 20
+  docker-compose logs --tail 10
+done
+
+# back to the root of the repo
+popd
+
diff --git a/.ci/cleanup.sh b/.ci/cleanup.sh
new file mode 100644
index 000000000..463b881ba
--- /dev/null
+++ b/.ci/cleanup.sh
@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+sudo rm -rf ./local_folder | true
+sudo rm -rf /export | true
+docker stop galaxy | true
+docker rm galaxy | true
diff --git a/.ci/compose_condor_docker.sh b/.ci/compose_condor_docker.sh
new file mode 100755
index 000000000..1cb816da7
--- /dev/null
+++ b/.ci/compose_condor_docker.sh
@@ -0,0 +1,57 @@
+#!/usr/bin/env bash
+
+set -o errexit
+
+echo '#### Start compose condor Docker testing ####'
+
+bash .ci/cleanup.sh
+
+source .ci/set_env.sh
+source .ci/functions.sh
+
+# The compose file recognises ENV vars to change the defaul behavior
+pushd ${COMPOSE_DIR}
+ln -sf .env_htcondor_docker .env
+
+# Galaxy needs to a full path for the the jobs, in- and outputs.
+# Do we want to run each job in it's own container and this container uses the host
+# container engine (not Docker in Docker) then the path to all files inside and outside
+# of the container needs to be the same.
+sudo mkdir /export
+sudo chmod 777 /export
+sudo chown 1450:1450 /export
+
+# start building this repo
+#git submodule update --init --recursive
+#sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
+
+popd
+source .ci/build_compose.sh
+pushd ${COMPOSE_DIR}
+
+source ./tags-for-compose-to-source.sh
+
+echo "Stopping SLURM container"
+docker-compose stop galaxy-slurm
+sleep 30
+
+docker-compose logs --tail 50
+docker ps
+
+sleep 10
+docker_exec_run shed-tools install -g "http://localhost:80" -a admin -t "$SAMPLE_TOOLS"
+
+popd
+
+echo '#### Start .ci/testing.sh ####'
+source .ci/testing.sh
+
+echo '#### Run a ton of BioBlend test against our servers ####'
+pushd $WORKING_DIR/test/bioblend/
+source ./test.sh 'compose'
+popd
+
+pushd ${COMPOSE_DIR}
+docker-compose down
+popd
+
diff --git a/.ci/compose_slurm.sh b/.ci/compose_slurm.sh
new file mode 100755
index 000000000..57223ae66
--- /dev/null
+++ b/.ci/compose_slurm.sh
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+
+set -o errexit
+
+echo '#### Start compose Slurm testing ####'
+
+bash .ci/cleanup.sh
+
+source .ci/set_env.sh
+source .ci/functions.sh
+
+# The compose file recognises ENV vars to change the defaul behavior
+pushd ${COMPOSE_DIR}
+ln -sf .env_slurm .env
+popd
+
+# start building this repo
+#git submodule update --init --recursive
+#sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
+
+source .ci/build_compose.sh
+
+echo "Stopping HT-Condor containers"
+docker-compose stop galaxy-htcondor galaxy-htcondor-executor galaxy-htcondor-executor-big
+sleep 30
+
+docker-compose logs --tail 50
+docker ps
+
+
+sleep 10
+docker_exec_run shed-tools install -g "http://localhost:80" -a admin -t "$SAMPLE_TOOLS"
+
diff --git a/.ci/compose_slurm_singularity.sh b/.ci/compose_slurm_singularity.sh
new file mode 100755
index 000000000..be2da64ad
--- /dev/null
+++ b/.ci/compose_slurm_singularity.sh
@@ -0,0 +1,81 @@
+#!/usr/bin/env bash
+
+set -o errexit
+
+source .ci/set_env.sh
+source .ci/functions.sh
+
+# The compose file recognises ENV vars to change the defaul behavior
+pushd ${COMPOSE_DIR}
+ln -sf .env_slurm_singularity .env
+popd
+
+# start building this repo
+#git submodule update --init --recursive
+#sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
+
+bash .ci/build_compose.sh
+
+# turn down the htcondor services
+echo "Stopping HT-Condor containers"
+docker-compose stop galaxy-htcondor galaxy-htcondor-executor galaxy-htcondor-executor-big
+sleep 30
+
+
+# docker-compose is already started and has pre-populated the /export dir
+# we now turn it down again and copy in an example tool with tool_conf.xml and
+# a test singularity image. If we copy this from the beginning, the magic Docker Galax startup
+# script will not work as it detects something in /export/
+echo "Downloading Singularity test files and images."
+docker-compose exec galaxy-web    mkdir -p /export/database/container_images/singularity/mulled/
+docker-compose exec galaxy-web    curl -L -o /export/database/container_images/singularity/mulled/samtools:1.4.1--0 https://github.com/bgruening/singularity-galaxy-tests/raw/master/samtools:1.4.1--0
+docker-compose exec galaxy-web    curl -L -o /export/cat_tool_conf.xml https://github.com/bgruening/singularity-galaxy-tests/raw/master/cat_tool_conf.xml
+docker-compose exec galaxy-web    curl -L -o /export/cat.xml https://github.com/bgruening/singularity-galaxy-tests/raw/master/cat.xml
+docker-compose exec galaxy-web    chown 1450:1450 /export/cat* /export/database/container_images/ -R
+docker-compose down
+sleep 20
+rm .env
+ln -sf .env_slurm_singularity2 .env
+
+docker-compose up -d
+
+until docker-compose exec galaxy-web ps -fC uwsgi
+do
+  echo "Starting up Singularity test container: sleeping for 40 seconds"
+  sleep 40
+  docker-compose logs
+done
+docker-compose logs galaxy-web
+sleep 30
+docker-compose logs galaxy-web
+sleep 30
+docker-compose logs galaxy-web
+echo "waiting until Galaxy is up"
+docker ps
+pip show ephemeris
+which galaxy-wait
+#galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 60 -v
+#docker-compose logs galaxy-web
+#galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 60 -v
+docker-compose logs galaxy-web
+sleep 500
+docker-compose logs
+echo "parsec init"
+parsec init --api_key admin --url $BIOBLEND_GALAXY_URL
+HISTORY_ID=$(parsec histories create_history | jq .id -r)
+DATASET_ID=$(parsec tools paste_content 'asdf' $HISTORY_ID | jq '.outputs[0].id' -r)
+OUTPUT_ID=$(parsec tools run_tool $HISTORY_ID cat '{"input1": {"src": "hda", "id": "'$DATASET_ID'"}}' | jq '.outputs | .[0].id' -r)
+sleep 10
+echo "run parsec jobs show_job"
+parsec jobs show_job --full_details $OUTPUT_ID
+# TODO: find a way to get a log trace that this tool actually was running with singularity
+#parsec jobs show_job --full_details $OUTPUT_ID | jq .stderr | grep singularity
+
+
+
+docker-compose logs --tail 50
+docker ps
+
+sleep 10
+docker_exec_run shed-tools install -g "http://localhost:80" -a admin -t "$SAMPLE_TOOLS"
+
diff --git a/.ci/functions.sh b/.ci/functions.sh
new file mode 100755
index 000000000..48419bdb2
--- /dev/null
+++ b/.ci/functions.sh
@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+
+## define a container size check function, first parameter is the container name, second the max allowed size in MB
+container_size_check () {
+
+  # check that the image size is not growing too much between releases
+  # the 19.05 monolithic image was around 1.500 MB
+  size=`docker image inspect $1 --format='{{.Size}}'`
+  size_in_mb=$(($size/(1024*1024)))
+  if [[ $size_in_mb -ge $2 ]]
+  then
+      echo "The new compiled image ($1) is larger than allowed. $size_in_mb vs. $2"
+      sleep 2
+      #exit
+  fi
+}
+
+# Define start functions
+docker_exec() {
+    cd $WORKING_DIR
+    docker-compose exec galaxy-web "$@"
+}
+docker_exec_run() {
+cd $WORKING_DIR
+    docker-compose exec galaxy-web "$@"
+}
+docker_run() {
+    cd $WORKING_DIR
+    docker-compose run "$@"
+}
diff --git a/.ci/kube.sh b/.ci/kube.sh
new file mode 100755
index 000000000..5f57527b8
--- /dev/null
+++ b/.ci/kube.sh
@@ -0,0 +1,49 @@
+#!/usr/bin/env bash
+
+set -o errexit
+
+source .ci/set_env.sh
+source .ci/functions.sh
+
+# setup k8s, we will do this before building Galaxy because it takes some time and hopefully we can do both in prallel
+gimme 1.11.1
+source ~/.gimme/envs/go1.11.1.env
+sudo ln -s /home/travis/.gimme/versions/go1.11.1.linux.amd64/bin/gofmt /usr/bin/gofmt
+sudo ln -s /home/travis/.gimme/versions/go1.11.1.linux.amd64/bin/go /usr/bin/go
+go version
+mkdir ../kubernetes
+wget -q -O - https://github.com/kubernetes/kubernetes/archive/master.tar.gz | tar xzf - --strip-components=1 -C ../kubernetes
+cd ../kubernetes
+# k8s API port is running by default on 8080 as Galaxy, can this to 8000
+export API_PORT=8000
+./hack/install-etcd.sh
+sudo ln -s `pwd`/third_party/etcd/etcd /usr/bin/etcd
+sudo ln -s `pwd`/third_party/etcd/etcdctl /usr/bin/etcdctl
+# this needs to run in backgroud later, for now try to see the output
+./hack/local-up-cluster.sh &
+cd ../docker-galaxy-stable
+
+# Installing kompose to convert the docker-compose YAML file
+
+# The compose file recognises ENV vars to change the defaul behavior
+cd ${COMPOSE_DIR}
+ln -sf .env_k8_native .env
+
+curl -L https://github.com/kubernetes-incubator/kompose/releases/download/v1.17.1/kompose-linux-amd64 -o kompose
+chmod +x kompose
+sudo mv ./kompose /usr/bin/kompose
+
+# start building this repo
+#git submodule update --init --recursive
+#sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
+
+
+bash .ci/build_compose.sh
+
+docker-compose logs --tail 50
+docker ps
+
+
+sleep 10
+docker_exec_run shed-tools install -g "http://localhost:80" -a admin -t "$SAMPLE_TOOLS"
+
diff --git a/.ci/monolithic.sh b/.ci/monolithic.sh
new file mode 100755
index 000000000..4bcec67a5
--- /dev/null
+++ b/.ci/monolithic.sh
@@ -0,0 +1,72 @@
+#!/usr/bin/env bash
+
+set -o errexit
+
+bash .ci/cleanup.sh
+
+source .ci/set_env.sh
+source .ci/functions.sh
+
+export DOCKER_RUN_CONTAINER="quay.io/bgruening/galaxy"
+INSTALL_REPO_ARG=""
+
+cd "$WORKING_DIR"
+docker build -t quay.io/bgruening/galaxy galaxy/
+
+container_size_check   quay.io/bgruening/galaxy  1550
+
+mkdir local_folder
+docker run -d -p 8080:80 -p 8021:21 -p 8022:22 \
+    --name galaxy \
+    --privileged=true \
+    -v `pwd`/local_folder:/export/ \
+    -e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
+    -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True \
+    -e GALAXY_CONFIG_ENABLE_USER_DELETION=True \
+    -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
+    -v /tmp/:/tmp/ \
+    quay.io/bgruening/galaxy
+
+sleep 30
+docker logs galaxy
+
+# Define start functions
+docker_exec() {
+  cd $WORKING_DIR
+  docker exec -t -i galaxy "$@"
+}
+docker_exec_run() {
+  cd $WORKING_DIR
+  docker run quay.io/bgruening/galaxy "$@"
+}
+docker_run() {
+  cd $WORKING_DIR
+  docker run "$@"
+}
+
+docker ps
+
+echo '#### Test submitting jobs to an external slurm cluster ####'
+pushd $WORKING_DIR/test/slurm/
+bash test.sh
+popd
+
+# Test submitting jobs to an external gridengine cluster
+# This test is not testing compose, thus disabled
+# TODO 19.05, need to enable this again!
+echo "skip SGE test, fix me"
+# cd $TRAVIS_BUILD_DIR/test/gridengine/ && bash test.sh && cd $WORKING_DIR
+
+echo '#### Start .ci/testing.sh ####'
+source .ci/testing.sh
+
+echo '### Run a ton of BioBlend test against our servers ####'
+pushd $WORKING_DIR/test/bioblend/
+source ./test.sh 'monolithic'
+popd ##cd $WORKING_DIR/
+
+
+echo '#### Test tool installation ####'
+docker_exec_run install-tools "$SAMPLE_TOOLS"
+
+bash .ci/cleanup.sh
diff --git a/.ci/set_env.sh b/.ci/set_env.sh
new file mode 100755
index 000000000..9166b842d
--- /dev/null
+++ b/.ci/set_env.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+export WORKING_DIR="${WORKING_DIR:=`pwd`}"
+
+export GALAXY_HOME=/home/galaxy
+export GALAXY_USER=admin@galaxy.org
+export GALAXY_USER_EMAIL=admin@galaxy.org
+export GALAXY_USER_PASSWD=admin
+export BIOBLEND_GALAXY_API_KEY=admin
+export BIOBLEND_GALAXY_URL=http://localhost:8080
+export COMPOSE_DIR="${WORKING_DIR}/compose"
+export SAMPLE_TOOLS=$GALAXY_HOME/ephemeris/sample_tool_list.yaml
diff --git a/.ci/setup.sh b/.ci/setup.sh
new file mode 100755
index 000000000..bce7a5692
--- /dev/null
+++ b/.ci/setup.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+set -e
+
+sudo apt-get update -qq
+sudo apt-get install docker-ce --no-install-recommends -y -o Dpkg::Options::="--force-confmiss" -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew"
+sudo apt-get install sshpass --no-install-recommends -y
+
+pip install ephemeris
+
+docker --version
+docker info
diff --git a/.ci/testing.sh b/.ci/testing.sh
new file mode 100755
index 000000000..4fffe01b2
--- /dev/null
+++ b/.ci/testing.sh
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+
+set -o errexit
+
+echo 'Waiting for Galaxy to come up.'
+galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 300
+
+curl -v --fail $BIOBLEND_GALAXY_URL/api/version
+
+# Test self-signed HTTPS
+docker_run -d --name httpstest -p 443:443 -e "USE_HTTPS=True" $DOCKER_RUN_CONTAINER
+# TODO 19.05
+# - sleep 90s && curl -v -k --fail https://127.0.0.1:443/api/version
+#- echo | openssl s_client -connect 127.0.0.1:443 2>/dev/null | openssl x509 -issuer -noout| grep selfsigned
+docker logs httpstest && docker stop httpstest && docker rm httpstest
+
+# Test FTP Server upload
+date > time.txt && curl -v --fail -T time.txt ftp://localhost:8021 --user $GALAXY_USER:$GALAXY_USER_PASSWD || true
+
+# Test FTP Server get
+curl -v --fail ftp://localhost:8021 --user $GALAXY_USER:$GALAXY_USER_PASSWD
+
+# Test CVMFS
+docker_exec bash -c "service autofs start"
+docker_exec bash -c "cvmfs_config chksetup"
+docker_exec bash -c "ls /cvmfs/data.galaxyproject.org/byhand"
+
+# Test SFTP Server
+sshpass -p $GALAXY_USER_PASSWD sftp -v -P 8022 -o User=$GALAXY_USER -o "StrictHostKeyChecking no" localhost <<< $'put time.txt'
+
+# Test the Conda installation
+docker_exec_run bash -c 'export PATH=$GALAXY_CONFIG_TOOL_DEPENDENCY_DIR/_conda/bin/:$PATH && conda --version && conda install samtools -c bioconda --yes'
+
diff --git a/.travis.yml b/.travis.yml
index 6e94b192a..545acd0cf 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,7 +8,7 @@ services:
 
 env:
   matrix:
-    - TOX_ENV=py27
+    - MONOLITHIC=True TOX_ENV=py27
     - COMPOSE_SLURM=True
     - COMPOSE_SLURM_SINGULARITY=True
     # Compose version with Condor submitting Docker jobs
@@ -25,349 +25,56 @@ git:
   submodules: false
 
 before_install:
-  - set -e
-  - export GALAXY_HOME=/home/galaxy
-  - export GALAXY_USER=admin@galaxy.org
-  - export GALAXY_USER_EMAIL=admin@galaxy.org
-  - export GALAXY_USER_PASSWD=admin
-  - export BIOBLEND_GALAXY_API_KEY=admin
-  - export BIOBLEND_GALAXY_URL=http://localhost:8080
-  - export COMPOSE_DIR="${TRAVIS_BUILD_DIR}/compose"
+  - export WORKING_DIR="$TRAVIS_BUILD_DIR"
+  - bash .ci/setup.sh
 
-  - sudo apt-get update -qq
-  - sudo apt-get install docker-ce --no-install-recommends -y -o Dpkg::Options::="--force-confmiss" -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew"
-  - sudo apt-get install sshpass --no-install-recommends -y
-  - pip install ephemeris
+  - git submodule update --init --recursive
+  - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
 
-  - docker --version
-  - docker info
-  # Build a k8s cluster
+  # Build and test the monolithic container
+  - |
+    if [ "${MONOLITHIC}" ]
+    then
+        bash .ci/monolithic.sh
+    fi
+
+  # Build and test the k8s compose containers
   - |
     if [ "${KUBE}" ]
     then
-      # setup k8s, we will do this before building Galaxy because it takes some time and hopefully we can do both in prallel
-      gimme 1.11.1
-      source ~/.gimme/envs/go1.11.1.env
-      sudo ln -s /home/travis/.gimme/versions/go1.11.1.linux.amd64/bin/gofmt /usr/bin/gofmt
-      sudo ln -s /home/travis/.gimme/versions/go1.11.1.linux.amd64/bin/go /usr/bin/go
-      go version
-      mkdir ../kubernetes
-      wget -q -O - https://github.com/kubernetes/kubernetes/archive/master.tar.gz | tar xzf - --strip-components=1 -C ../kubernetes
-      cd ../kubernetes
-      # k8s API port is running by default on 8080 as Galaxy, can this to 8000
-      export API_PORT=8000
-      ./hack/install-etcd.sh
-      sudo ln -s `pwd`/third_party/etcd/etcd /usr/bin/etcd
-      sudo ln -s `pwd`/third_party/etcd/etcdctl /usr/bin/etcdctl
-      # this needs to run in backgroud later, for now try to see the output
-      ./hack/local-up-cluster.sh &
-      cd ../docker-galaxy-stable
+        bash .ci/kube.sh
     fi
 
 
-  # load all configurations needed for SLURM testing
+  # Build and test the compose SLURM enabled containers
   - |
     if [ "${COMPOSE_SLURM}" ]
     then
-      # The compose file recognises ENV vars to change the defaul behavior
-      cd ${COMPOSE_DIR}
-      ln -sf .env_slurm .env
+        bash .ci/compose_slurm.sh
     fi
 
-  # load all configurations needed for SLURM testing
+  # Build and test the compose SLURM enabled containers with Singularity dependency resolver
   - |
     if [ "${COMPOSE_SLURM_SINGULARITY}" ]
     then
-      # The compose file recognises ENV vars to change the defaul behavior
-      cd ${COMPOSE_DIR}
-      ln -sf .env_slurm_singularity .env
+        bash .ci/compose_slurm_singularity.sh
     fi
 
-  # load all configurations needed for Condor and Docker
+  # Build and test the compose ht-condor enabled containers with Docker dependency resolver
   - |
     if [ "${COMPOSE_CONDOR_DOCKER}" ]
     then
-      # The compose file recognises ENV vars to change the defaul behavior
-      cd ${COMPOSE_DIR}
-      ln -sf .env_htcondor_docker .env
-
-      # Galaxy needs to a full path for the the jobs, in- and outputs.
-      # Do we want to run each job in it's own container and this container uses the host
-      # container engine (not Docker in Docker) then the path to all files inside and outside
-      # of the container needs to be the same.
-      sudo mkdir /export
-      sudo chmod 777 /export
-      sudo chown 1450:1450 /export
-    fi
-
-  # Installing kompose to convert the docker-compose YAML file
-  - |
-    if [ "${KUBE}" ]
-    then
-        # The compose file recognises ENV vars to change the defaul behavior
-        cd ${COMPOSE_DIR}
-        ln -sf .env_k8_native .env
-
-        curl -L https://github.com/kubernetes-incubator/kompose/releases/download/v1.17.1/kompose-linux-amd64 -o kompose
-        chmod +x kompose
-        sudo mv ./kompose /usr/bin/kompose
+        bash .ci/compose_condor_docker.sh
     fi
 
-  # start building this repo
-  - git submodule update --init --recursive
-  - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
-  - |
-    ## define a container size check function, first parameter is the container name, second the max allowed size in MB
-    container_size_check () {
-
-        # check that the image size is not growing too much between releases
-        # the 19.05 monolithic image was around 1.500 MB
-        size=`docker image inspect $1 --format='{{.Size}}'`
-        size_in_mb=$(($size/(1024*1024)))
-        if [[ $size_in_mb -ge $2 ]]
-        then
-            echo "The new compiled image ($1) is larger than allowed. $size_in_mb vs. $2"
-            sleep 2
-            #exit
-        fi
-    }
-
-    if [ "${COMPOSE_SLURM}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${KUBE}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]
-    then
-        pip install docker-compose galaxy-parsec
-        export WORKING_DIR="$TRAVIS_BUILD_DIR/compose"
-        export DOCKER_RUN_CONTAINER="galaxy-web"
-        INSTALL_REPO_ARG="--galaxy-url http://localhost:80"
-        SAMPLE_TOOLS=/export/config/sample_tool_list.yaml
-        cd "$WORKING_DIR"
-        # For build script
-        export CONTAINER_REGISTRY=quay.io/
-        export CONTAINER_USER=bgruening
-        ./build-orchestration-images.sh --no-push --condor --grafana --slurm --k8s
-        source ./tags-for-compose-to-source.sh
-
-        container_size_check   quay.io/bgruening/galaxy-base:$TAG               350 
-        container_size_check   quay.io/bgruening/galaxy-web:$TAG                650
-        container_size_check   quay.io/bgruening/galaxy-htcondor-base:$TAG      280
-
-        export COMPOSE_PROJECT_NAME=galaxy_compose
-        docker-compose up -d
-
-        until docker-compose exec galaxy-web ps -fC uwsgi
-        do
-          echo "sleeping for 20 seconds"
-          sleep 20
-          docker-compose logs --tail 10
-        done
-
-        if [ "${COMPOSE_CONDOR_DOCKER}" ]
-        then
-            # turn down the slurm service
-            echo "Stopping SLURM container"
-            docker-compose stop galaxy-slurm
-            sleep 30
-        fi
-
-        if [ "${COMPOSE_SLURM}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]
-        then
-            # turn down the htcondor services
-            echo "Stopping HT-Condor containers"
-            docker-compose stop galaxy-htcondor galaxy-htcondor-executor galaxy-htcondor-executor-big
-            sleep 30
-        fi
-
-        if [ "${COMPOSE_SLURM_SINGULARITY}" ]
-        then
-            # docker-compose is already started and has pre-populated the /export dir
-            # we now turn it down again and copy in an example tool with tool_conf.xml and
-            # a test singularity image. If we copy this from the beginning, the magic Docker Galax startup
-            # script will not work as it detects something in /export/
-            echo "Downloading Singularity test files and images."
-            docker-compose exec galaxy-web    mkdir -p /export/database/container_images/singularity/mulled/
-            docker-compose exec galaxy-web    curl -L -o /export/database/container_images/singularity/mulled/samtools:1.4.1--0 https://github.com/bgruening/singularity-galaxy-tests/raw/master/samtools:1.4.1--0
-            docker-compose exec galaxy-web    curl -L -o /export/cat_tool_conf.xml https://github.com/bgruening/singularity-galaxy-tests/raw/master/cat_tool_conf.xml
-            docker-compose exec galaxy-web    curl -L -o /export/cat.xml https://github.com/bgruening/singularity-galaxy-tests/raw/master/cat.xml
-            docker-compose exec galaxy-web    chown 1450:1450 /export/cat* /export/database/container_images/ -R
-            docker-compose down
-            sleep 20
-            rm .env
-            ln -sf .env_slurm_singularity2 .env
-
-            docker-compose up -d
 
-            until docker-compose exec galaxy-web ps -fC uwsgi
-            do
-              echo "Starting up Singularity test container: sleeping for 40 seconds"
-              sleep 40
-              docker-compose logs
-            done
-            docker-compose logs galaxy-web
-            sleep 30
-            docker-compose logs galaxy-web
-            sleep 30
-            docker-compose logs galaxy-web
-            echo "waiting until Galaxy is up"
-            docker ps
-            pip show ephemeris
-            which galaxy-wait
-            #galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 60 -v
-            #docker-compose logs galaxy-web
-            #galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 60 -v
-            docker-compose logs galaxy-web
-            sleep 500
-            docker-compose logs
-            echo "parsec init"
-            parsec init --api_key admin --url $BIOBLEND_GALAXY_URL
-            HISTORY_ID=$(parsec histories create_history | jq .id -r)
-            DATASET_ID=$(parsec tools paste_content 'asdf' $HISTORY_ID | jq '.outputs[0].id' -r)
-            OUTPUT_ID=$(parsec tools run_tool $HISTORY_ID cat '{"input1": {"src": "hda", "id": "'$DATASET_ID'"}}' | jq '.outputs | .[0].id' -r)
-            sleep 10
-            echo "run parsec jobs show_job"
-            parsec jobs show_job --full_details $OUTPUT_ID
-            # TODO: find a way to get a log trace that this tool actually was running with singularity
-            #parsec jobs show_job --full_details $OUTPUT_ID | jq .stderr | grep singularity
 
-        fi
 
-        docker-compose logs --tail 50
-        # Define start functions
-        docker_exec() {
-          cd $WORKING_DIR
-          docker-compose exec galaxy-web "$@"
-        }
-        docker_exec_run() {
-          cd $WORKING_DIR
-          docker-compose exec galaxy-web "$@"
-        }
-        docker_run() {
-          cd $WORKING_DIR
-          docker-compose run "$@"
-        }
-    else
-        export WORKING_DIR="$TRAVIS_BUILD_DIR"
-        export DOCKER_RUN_CONTAINER="quay.io/bgruening/galaxy"
-        INSTALL_REPO_ARG=""
-        SAMPLE_TOOLS=$GALAXY_HOME/ephemeris/sample_tool_list.yaml
-        cd "$WORKING_DIR"
-        docker build -t quay.io/bgruening/galaxy galaxy/
 
-        container_size_check   quay.io/bgruening/galaxy  1500
-
-        mkdir local_folder
-        docker run -d -p 8080:80 -p 8021:21 -p 8022:22 \
-            --name galaxy \
-            --privileged=true \
-            -v `pwd`/local_folder:/export/ \
-            -e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
-            -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True \
-            -e GALAXY_CONFIG_ENABLE_USER_DELETION=True \
-            -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
-            -v /tmp/:/tmp/ \
-            quay.io/bgruening/galaxy
-
-        sleep 30
-        docker logs galaxy
-        # Define start functions
-        docker_exec() {
-          cd $WORKING_DIR
-          docker exec -t -i galaxy "$@"
-        }
-        docker_exec_run() {
-          cd $WORKING_DIR
-          docker run quay.io/bgruening/galaxy "$@"
-        }
-        docker_run() {
-          cd $WORKING_DIR
-          docker run "$@"
-        }
-
-    fi
-  - docker ps
 
 script:
-  - set -e
-  # Test submitting jobs to an external slurm cluster
-  - |
-      if [ ! "${COMPOSE_SLURM}" ] && [ ! "${KUBE}" ] && [ ! "${COMPOSE_CONDOR_DOCKER}" ] && [ ! "${COMPOSE_SLURM_SINGULARITY}" ]
-      then
-        # For compose slurm is already included and thus tested
-        cd $TRAVIS_BUILD_DIR/test/slurm/ && bash test.sh && cd $WORKING_DIR
-      fi
-  # Test submitting jobs to an external gridengine cluster
-  - |
-      if [ ! "${COMPOSE_SLURM}" ] && [ ! "${KUBE}" ] && [ ! "${COMPOSE_CONDOR_DOCKER}" ] && [ ! "${COMPOSE_SLURM_SINGULARITY}" ]
-      then
-        # This test is not testing compose, thus disabled
-        # TODO 19.05, need to enable this again!
-        echo "skip SGE test, fix me"
-        # cd $TRAVIS_BUILD_DIR/test/gridengine/ && bash test.sh && cd $WORKING_DIR
-      fi
-  # Test Web api
-  - |
-      if [ "${COMPOSE_CONDOR_DOCKER}" ]
-      then
-        docker-compose logs --tail 50
-      fi
-
-  - echo 'Waiting for Galaxy to come up.'
-  - galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 300
-
-  - curl -v --fail $BIOBLEND_GALAXY_URL/api/version
-
-  # Test self-signed HTTPS
-  - docker_run -d --name httpstest -p 443:443 -e "USE_HTTPS=True" $DOCKER_RUN_CONTAINER
-  # TODO 19.05
-  # - sleep 90s && curl -v -k --fail https://127.0.0.1:443/api/version
-  #- echo | openssl s_client -connect 127.0.0.1:443 2>/dev/null | openssl x509 -issuer -noout| grep selfsigned
-  - docker logs httpstest && docker stop httpstest && docker rm httpstest
-
-  # Test FTP Server upload
-  - date > time.txt && curl -v --fail -T time.txt ftp://localhost:8021 --user $GALAXY_USER:$GALAXY_USER_PASSWD || true
-  # Test FTP Server get
-  - curl -v --fail ftp://localhost:8021 --user $GALAXY_USER:$GALAXY_USER_PASSWD
-
-  # Test CVMFS
-  - docker_exec bash -c "service autofs start"
-  - docker_exec bash -c "cvmfs_config chksetup"
-  - docker_exec bash -c "ls /cvmfs/data.galaxyproject.org/byhand"
 
-  # Test SFTP Server
-  - sshpass -p $GALAXY_USER_PASSWD sftp -v -P 8022 -o User=$GALAXY_USER -o "StrictHostKeyChecking no" localhost <<< $'put time.txt'
 
-  # Run a ton of BioBlend test against our servers.
-  - cd $TRAVIS_BUILD_DIR/test/bioblend/ && . ./test.sh && cd $WORKING_DIR/
-
-  # not working anymore in 18.01
-  # executing: /galaxy_venv/bin/uwsgi --yaml /etc/galaxy/galaxy.yml --master --daemonize2 galaxy.log --pidfile2 galaxy.pid  --log-file=galaxy_install.log --pid-file=galaxy_install.pid
-  # [uWSGI] getting YAML configuration from /etc/galaxy/galaxy.yml
-  # /galaxy_venv/bin/python: unrecognized option '--log-file=galaxy_install.log'
-  # getopt_long() error
-  # cat: galaxy_install.pid: No such file or directory
-  # tail: cannot open ‘galaxy_install.log’ for reading: No such file or directory
-  #- |
-  #  if [ "${COMPOSE_SLURM}" ] || [ "${KUBE}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]
-  #  then
-  #      # Test without install-repository wrapper
-  #      sleep 10
-  #      docker_exec_run bash -c 'cd $GALAXY_ROOT && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
-  #  fi
-
-
-  # Test the 'new' tool installation script
-#  - docker_exec bash -c "install-tools $GALAXY_HOME/ephemeris/sample_tool_list.yaml"
-  - |
-    if [ "${COMPOSE_SLURM}" ] || [ "${KUBE}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]
-    then
-        # Compose uses the online installer (uses the running instance)
-        sleep 10
-        docker_exec_run shed-tools install -g "http://localhost:80" -a admin -t "$SAMPLE_TOOLS"
-    else
-      docker_exec_run install-tools "$SAMPLE_TOOLS"
-    fi
-  # Test the Conda installation
-  - docker_exec_run bash -c 'export PATH=$GALAXY_CONFIG_TOOL_DEPENDENCY_DIR/_conda/bin/:$PATH && conda --version && conda install samtools -c bioconda --yes'
-  # Test Docker in Docker, used by Interactive Environments; This needs to be at the end as Docker takes some time to start.
-  #- docker_exec docker info
   # Check if the database image matches the current galaxy version
   - |
       if [ "${COMPOSE_SLURM}" ] || [ "${KUBE}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]
diff --git a/README.md b/README.md
index c3d3b929e..7f30a8001 100644
--- a/README.md
+++ b/README.md
@@ -59,6 +59,7 @@ The Image is based on [Ubuntu 14.04 LTS](http://releases.ubuntu.com/14.04/) and
 - [Integrating non-Tool Shed tools into the container](#Integrating-non-Tool-Shed-tools-into-the-container)
 - [Users & Passwords](#Users-Passwords)
 - [Development](#Development)
+  - [Testing](#Testing)
 - [Requirements](#Requirements)
 - [History](#History)
 - [Support & Bug Reports](#Support-Bug-Reports)
@@ -774,6 +775,18 @@ If you simply want to change the Galaxy repository and/or the Galaxy branch, fro
  --build-arg GALAXY_REPO=https://github.com/manabuishii/galaxy
 ```
 
+## Testing the images
+
+You can run our test against the newly build images with our test scripts. Please note that for a few tests we currently need to run commands with sudo.
+We also assume you have Docker installed.
+
+Testing the monolithic container:
+
+```bash
+.ci/monolithic.sh
+```
+
+
 # Requirements <a name="Requirements" /> [[toc]](#toc)
 
 - [Docker](https://www.docker.io/gettingstarted/#h_installation)
diff --git a/galaxy/Dockerfile b/galaxy/Dockerfile
index 66ec6aa22..8d13f122f 100644
--- a/galaxy/Dockerfile
+++ b/galaxy/Dockerfile
@@ -99,7 +99,7 @@ RUN groupadd -r postgres -g $GALAXY_POSTGRES_GID \
     && apt-get install git --no-install-recommends -y \
     && apt-get install gridengine-common gridengine-drmaa1.0 --no-install-recommends -y \
     && apt-get install rabbitmq-server --no-install-recommends -y \
-    && apt-get install --no-install-recommends -y libswitch-perl supervisor \
+    && apt-get install --no-install-recommends -y uuid-runtime libswitch-perl supervisor \
     && apt-get purge -y software-properties-common gpg-agent apt-transport-https python3-minimal  \
     && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \
     && mkdir -p /etc/supervisor/conf.d/ /var/log/supervisor/ \
@@ -197,7 +197,9 @@ RUN mkdir -p /shed_tools $EXPORT_DIR/ftp/ \
         --extra-vars galaxy_config_dir=$GALAXY_CONFIG_DIR \
         --extra-vars galaxy_job_conf_path=$GALAXY_CONFIG_JOB_CONFIG_FILE \
         --extra-vars galaxy_job_metrics_conf_path=$GALAXY_CONFIG_JOB_METRICS_CONFIG_FILE \
-        --extra-vars supervisor_manage_slurm="" \
+        --extra-vars supervisor_manage_slurm=True \
+        --extra-vars supervisor_slurm_autostart=False \
+        --extra-vars supervisor_condor_autostart=False \
         --extra-vars galaxy_extras_config_condor=True \
         --extra-vars galaxy_extras_config_condor_docker=True \
         --extra-vars galaxy_extras_config_rabbitmq=True \
diff --git a/galaxy/roles/galaxyprojectdotorg.galaxyextras b/galaxy/roles/galaxyprojectdotorg.galaxyextras
index 9aa0286fc..9677970ee 160000
--- a/galaxy/roles/galaxyprojectdotorg.galaxyextras
+++ b/galaxy/roles/galaxyprojectdotorg.galaxyextras
@@ -1 +1 @@
-Subproject commit 9aa0286fc5e50c321950fec1285b7e10929aa25d
+Subproject commit 9677970eee69660a30e73bed251d2482959aab61
diff --git a/test/bioblend/test.sh b/test/bioblend/test.sh
index 1f84d7add..3d54d7680 100644
--- a/test/bioblend/test.sh
+++ b/test/bioblend/test.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
-if [ "${COMPOSE_SLURM}" ] || [ "${KUBE}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]
+
+if [ $1 -eq "compose" ]
 then
     docker_exec bash -c 'cd /home/galaxy ;
     . /galaxy_venv/bin/activate ;
diff --git a/test/slurm/Dockerfile b/test/slurm/Dockerfile
index 76495a16d..53c74bbe5 100644
--- a/test/slurm/Dockerfile
+++ b/test/slurm/Dockerfile
@@ -11,7 +11,7 @@ RUN apt-get update -qq && apt-get install -y --no-install-recommends \
     apt install -y docker-ce && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ && \
     adduser galaxy &&\
-    /usr/sbin/create-munge-key &&\
+    yes | /usr/sbin/create-munge-key &&\
     touch /var/log/slurm-llnl/slurmctld.log /var/log/slurm-llnl/slurmd.log &&\
     mkdir /tmp/slurm
 
diff --git a/test/slurm/startup.sh b/test/slurm/startup.sh
index 9b6cb4439..09c22ed91 100644
--- a/test/slurm/startup.sh
+++ b/test/slurm/startup.sh
@@ -18,7 +18,6 @@ if [ ! -f "$SLURM_CONF_PATH" ]
   then
     python /usr/local/bin/configure_slurm.py
     cp /etc/slurm-llnl/slurm.conf "$SLURM_CONF_PATH"
-    rm /etc/slurm-llnl/slurm.conf
 fi
 if [ ! -f "$GALAXY_DIR"/.venv ]
   then
diff --git a/test/slurm/test.sh b/test/slurm/test.sh
index d966f6789..122376ccc 100644
--- a/test/slurm/test.sh
+++ b/test/slurm/test.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-set -x
+set -o errexit
 # Test that jobs run successfully on an external slurm cluster
 
 # We use a temporary directory as an export dir that will hold the shared data between
@@ -36,4 +36,5 @@ sleep 60s
 docker exec galaxy-slurm-test su - galaxy -c 'srun hostname' | grep slurm
 docker stop galaxy-slurm-test slurm
 docker rm galaxy-slurm-test slurm
+
 # TODO: Run a galaxy tool and check it runs on the cluster