diff --git a/.github/workflows/compose.yml b/.github/workflows/compose.yml
index 2dbf435f6..c076434d3 100644
--- a/.github/workflows/compose.yml
+++ b/.github/workflows/compose.yml
@@ -2,7 +2,7 @@ name: build-and-test
 on: [push]
 jobs:
   build_container_base:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
       - name: Checkout
         uses: actions/checkout@v2
@@ -120,7 +120,7 @@ jobs:
             --build-arg IMAGE_TAG=${{ steps.image_tag.outputs.image_tag }} \
             --build-arg DOCKER_REGISTRY=${{ secrets.docker_registry }} \
             --build-arg DOCKER_REGISTRY_USERNAME=${{ secrets.docker_registry_username }} \
-            --build-arg GALAXY_REPO=https://github.com/andreassko/galaxy \
+            --build-arg GALAXY_REPO=https://github.com/galaxyproject/galaxy \
             ${{ matrix.image.subdir }}${{ matrix.image.name }} && break || echo "Fail.. Retrying"
           done;
         shell: bash
@@ -164,6 +164,7 @@ jobs:
             files: -f docker-compose.yml -f docker-compose.k8s.yml
             exclude_test:
               - bioblend
+              - workflow_example1
               - workflow_ard
               - workflow_mapping_by_sequencing
               - selenium
@@ -232,13 +233,13 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v2
       - name: Set image tag in env
-        run: echo "::set-env name=IMAGE_TAG::${GITHUB_REF#refs/heads/}"
+        run: echo "IMAGE_TAG=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
       - name: Master branch - Set image to to 'latest'
         if: github.ref == 'refs/heads/master'
-        run: echo "::set-env name=IMAGE_TAG::latest"
+        run: echo "IMAGE_TAG=latest" >> $GITHUB_ENV
       - name: Set WORKFLOWS env for worfklows-test
         if: matrix.test.workflow
-        run: echo "::set-env name=WORKFLOWS::${{ matrix.test.workflow }}"
+        run: echo "WORKFLOWS=${{ matrix.test.workflow }}" >> $GITHUB_ENV
       - name: Run tests for the first time
         if: steps.run_check.outputs.run
         run: |
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 63693b86d..36692201a 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -16,7 +16,7 @@ jobs:
         level: warning
         pattern: "*.sh"
     - name: Run hadolint with reviewdog
-      uses: reviewdog/action-hadolint@v1
+      uses: reviewdog/action-hadolint@v1.16.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         reporter: github-check
diff --git a/.github/workflows/pull-request.yml b/.github/workflows/pull-request.yml
index 9eb289190..12baa530c 100644
--- a/.github/workflows/pull-request.yml
+++ b/.github/workflows/pull-request.yml
@@ -2,7 +2,7 @@ name: pr-test
 on: pull_request
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
         infrastructure:
@@ -30,6 +30,7 @@ jobs:
             exclude_test:
               - workflow_example1
               - workflow_mapping_by_sequencing
+              - workflow_ard
           # - name: galaxy-pulsar-mq
           #   files: -f docker-compose.yml -f docker-compose.pulsar.yml -f docker-compose.pulsar.mq.yml
           #   exclude_test:
@@ -41,6 +42,7 @@ jobs:
               - bioblend
               - workflow_ard
               - workflow_mapping_by_sequencing
+              - workflow_example1
               - selenium
           - name: galaxy-singularity
             files: -f docker-compose.yml -f docker-compose.singularity.yml
@@ -108,7 +110,7 @@ jobs:
         uses: actions/checkout@v2
       - name: Set WORKFLOWS env for worfklows-test
         if: matrix.test.workflow
-        run: echo "::set-env name=WORKFLOWS::${{ matrix.test.workflow }}"
+        run: echo "WORKFLOWS=${{ matrix.test.workflow }}" >> $GITHUB_ENV
       - name: Build galaxy-container-base
         env:
           image_name: galaxy-container-base
@@ -142,7 +144,7 @@ jobs:
             echo "Removing export directory if existent";
             sudo rm -rf export
             set +e
-            docker-compose ${{ matrix.infrastructure.files }} ${{ matrix.test.files }} build --build-arg IMAGE_TAG=ci-testing --build-arg GALAXY_REPO=https://github.com/andreassko/galaxy
+            docker-compose ${{ matrix.infrastructure.files }} ${{ matrix.test.files }} build --build-arg IMAGE_TAG=ci-testing --build-arg GALAXY_REPO=https://github.com/galaxyproject/galaxy
             docker-compose ${{ matrix.infrastructure.files }} ${{ matrix.test.files }} up ${{ matrix.infrastructure.options }} --exit-code-from ${{ matrix.test.exit-from }}
             test_exit_code=$?
             error_exit_codes_count=$(expr $(docker ps -a --filter exited=1 | wc -l) - 1)
diff --git a/.github/workflows/single.sh b/.github/workflows/single.sh
new file mode 100755
index 000000000..446d867ae
--- /dev/null
+++ b/.github/workflows/single.sh
@@ -0,0 +1,139 @@
+#!/bin/bash
+set -ex
+
+export GALAXY_HOME=/home/galaxy
+export GALAXY_USER=admin@galaxy.org
+export GALAXY_USER_EMAIL=admin@galaxy.org
+export GALAXY_USER_PASSWD=password
+export BIOBLEND_GALAXY_API_KEY=fakekey
+export BIOBLEND_GALAXY_URL=http://localhost:8080
+
+sudo apt-get update -qq
+#sudo apt-get install docker-ce --no-install-recommends -y -o Dpkg::Options::="--force-confmiss" -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew"
+sudo apt-get install sshpass --no-install-recommends -y
+
+pip3 install ephemeris
+
+docker --version
+docker info
+
+# start building this repo
+git submodule update --init --recursive
+sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
+
+## define a container size check function, first parameter is the container name, second the max allowed size in MB
+container_size_check () {
+
+    # check that the image size is not growing too much between releases
+    # the 19.05 monolithic image was around 1.500 MB
+    size="${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. $2"
+        sleep 2
+        #exit
+    fi
+}
+
+export WORKING_DIR=${GITHUB_WORKSPACE:-$PWD}
+
+export DOCKER_RUN_CONTAINER="quay.io/bgruening/galaxy"
+SAMPLE_TOOLS=$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 "$WORKING_DIR"
+      docker exec galaxy "$@"
+}
+docker_exec_run() {
+   cd "$WORKING_DIR"
+   docker run quay.io/bgruening/galaxy "$@"
+}
+docker_run() {
+   cd "$WORKING_DIR"
+   docker run "$@"
+}
+
+docker ps
+
+# Test submitting jobs to an external slurm cluster
+cd "${WORKING_DIR}/test/slurm/" && bash test.sh && cd "$WORKING_DIR"
+
+# Test submitting jobs to an external gridengine cluster
+# TODO 19.05, need to enable this again!
+# - cd $WORKING_DIR/test/gridengine/ && bash test.sh && cd $WORKING_DIR
+
+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
+# FIXME passive mode does not work, it would require the container to run with --net=host
+#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 <<< $'put time.txt'
+
+# Run a ton of BioBlend test against our servers.
+cd "$WORKING_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 $GALAXY_ROOT && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
+#  fi
+
+
+# Test the 'new' tool installation script
+docker_exec install-tools "$SAMPLE_TOOLS"
+# 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'
+
+
+docker stop galaxy
+docker rm -f galaxy
+docker rmi -f $DOCKER_RUN_CONTAINER
diff --git a/.github/workflows/single_container.yml b/.github/workflows/single_container.yml
new file mode 100644
index 000000000..31223bc18
--- /dev/null
+++ b/.github/workflows/single_container.yml
@@ -0,0 +1,16 @@
+name: Single Container Test
+on: [push]
+jobs:
+  build_and_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Build and Test
+      run: bash .github/workflows/single.sh
diff --git a/.travis.yml b/.travis.yml
index 694321b4c..4353fad27 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -40,6 +40,11 @@ before_install:
   # start building this repo
   - git submodule update --init --recursive
   - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
+  - export WORKING_DIR="$TRAVIS_BUILD_DIR"
+  - export DOCKER_RUN_CONTAINER="quay.io/bgruening/galaxy"
+  - export INSTALL_REPO_ARG=""
+  - export SAMPLE_TOOLS=$GALAXY_HOME/ephemeris/sample_tool_list.yaml
+  - travis_wait 30 cd "$WORKING_DIR" && docker build -t quay.io/bgruening/galaxy galaxy/
   - |
     ## define a container size check function, first parameter is the container name, second the max allowed size in MB
     container_size_check () {
@@ -55,14 +60,6 @@ before_install:
             #exit
         fi
     }
-
-    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
diff --git a/README.md b/README.md
index a64c50650..6e23c7b71 100644
--- a/README.md
+++ b/README.md
@@ -993,6 +993,8 @@ If you simply want to change the Galaxy repository and/or the Galaxy branch, fro
    - Featuring Galaxy 20.05
    - Completely reworked compose setup
    - The default admin password and apikey (`GALAXY_DEFAULT_ADMIN_PASSWORD` and `GALAXY_DEFAULT_ADMIN_KEY`) have changed: the password is now `password` (instead of `admin`) and the apikey `fakekey` (instead of `admin`).
+- 20.09:
+   - Featuring Galaxy 20.09
 
 # Support & Bug Reports <a name="Support-Bug-Reports" /> [[toc]](#toc)
 
diff --git a/compose/README.md b/compose/README.md
index 3007747d0..d73d39a5d 100644
--- a/compose/README.md
+++ b/compose/README.md
@@ -151,9 +151,9 @@ All options are discussed under [configuration reference](#configuration-referen
 
 ### Use specific Galaxy version or Docker images
 The `IMAGE_TAG` environment variable allows to use specific versions of the
-setup. Say, you want to stay with Galaxy v20.05 for now:
+setup. Say, you want to stay with Galaxy v20.09 for now:
 
-> export IMAGE_TAG=20.05
+> export IMAGE_TAG=20.09
 > docker-compose up
 
 Without setting this variable, you will always get updated to the newest
@@ -378,7 +378,7 @@ The following are settings specific to this docker-compose setup:
 | `GALAXY_K8S_DOCKER_REPO_DEFAULT` | The Docker Repo/Registry to use if the resolver could not resolve the proper image for a job. Defaults to `docker.io`. |
 | `GALAXY_K8S_DOCKER_OWNER_DEFAULT` | The Owner/Username to use if the resolver could not resolve the proper image for a job. Is not set by default. |
 | `GALAXY_K8S_DOCKER_IMAGE_DEFAULT` | The Image to use if the resolver could not resolve the proper image for a job. Defaults to `ubuntu`. |
-| `GALAXY_K8S_DOCKER_TAG_DEFAULT` | The Image Tag to use if the resolver could not resolve the proper image for a job. Defaults to `18.04`. |
+| `GALAXY_K8S_DOCKER_TAG_DEFAULT` | The Image Tag to use if the resolver could not resolve the proper image for a job. Defaults to `20.04`. |
 
 ### HTCondor
 | Variable                    | Description                                                                                                        |
@@ -393,3 +393,21 @@ The following are settings specific to this docker-compose setup:
 | `SLURM_NODE_CPUS`         | Number of CPUs per node. Defaults to 1. |
 | `SLURM_NODE_MEMORY`       | Amount of memory per node. Defaults to 1024. |
 | `SLURM_NODE_HOSTNAME`     | Docker Compose adds a prefix in front of the container names by default. Change this value to the name of your setup and `_slurm_node` (e.g. `compose_slurm_node`) to ensure a correct mapping of the Slurm nodes. |
+
+### Github Workflow Tests (Branch 20.09)
+| Setup                  | bioblend           | workflow ard       | workflow mapping_by_sequencing | workflow wf3-shed-tools (example1) | selenium           |
+|------------------------|--------------------|--------------------|--------------------------------|------------------------------------|--------------------|
+| Galaxy Base            | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark:             | :x:                                | :heavy_check_mark: |
+| Galaxy Proxy Prefix    | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark:             | :x:                                | :heavy_check_mark: |
+| HTCondor               | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark:             | :x:                                | :heavy_check_mark: |
+| Slurm                  | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark:             | :x:                                | :heavy_check_mark: |
+| Pulsar                 | :heavy_check_mark: | :x:                | :x:                            | :x:                                | :heavy_check_mark: |
+| k8s                    | :x:                | :x:                | :x:                            | :x:                                | :x:                |
+| Singularity            | :x:                | :x:                | :x:                            | :heavy_check_mark:                 | :x:                |
+| Slurm + Singularity    | :x:                | :x:                | :x:                            | :heavy_check_mark:                 | :x:                |
+| HTCondor + Singularity | :x:                | :x:                | :x:                            | :heavy_check_mark:                 | :x:                |
+
+
+Implemented: :heavy_check_mark:   
+Not Implemented: :x:
+
diff --git a/compose/base-images/galaxy-cluster-base/Dockerfile b/compose/base-images/galaxy-cluster-base/Dockerfile
index f9d668009..ff7c91cce 100644
--- a/compose/base-images/galaxy-cluster-base/Dockerfile
+++ b/compose/base-images/galaxy-cluster-base/Dockerfile
@@ -20,11 +20,11 @@ ENV MUNGER_USER=munge \
     MUNGE_GID=1200
 RUN groupadd -r $MUNGER_USER -g $MUNGE_GID \
     && useradd -u $MUNGE_UID -r -g $MUNGER_USER $MUNGER_USER \
-    && echo "deb http://ppa.launchpad.net/natefoo/slurm-drmaa/ubuntu bionic main" >> /etc/apt/sources.list \
-    && echo "deb-src http://ppa.launchpad.net/natefoo/slurm-drmaa/ubuntu bionic main" >> /etc/apt/sources.list \
+    && echo "deb http://ppa.launchpad.net/natefoo/slurm-drmaa/ubuntu focal main" >> /etc/apt/sources.list \
+    && echo "deb-src http://ppa.launchpad.net/natefoo/slurm-drmaa/ubuntu focal main" >> /etc/apt/sources.list \
     && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 8DE68488997C5C6BA19021136F2CC56412788738 \
     && apt update \
-    && apt install --no-install-recommends slurm-client slurmd slurmctld slurm-drmaa1 -y \
+    && apt install --no-install-recommends python3-distutils slurm-client slurmd slurmctld slurm-drmaa1 -y \
     && apt --no-install-recommends install munge libmunge-dev -y \
     && ln -s /usr/lib/slurm-drmaa/lib/libdrmaa.so.1 /usr/lib/slurm-drmaa/lib/libdrmaa.so \
     && /usr/bin/common_cleanup.sh
diff --git a/compose/base-images/galaxy-container-base/Dockerfile b/compose/base-images/galaxy-container-base/Dockerfile
index 20fa3743f..6cf33a516 100644
--- a/compose/base-images/galaxy-container-base/Dockerfile
+++ b/compose/base-images/galaxy-container-base/Dockerfile
@@ -1,4 +1,4 @@
-FROM buildpack-deps:18.04  as build_singularity
+FROM buildpack-deps:20.04  as build_singularity
 
 COPY ./files/common_cleanup.sh /usr/bin/common_cleanup.sh
 
@@ -21,12 +21,12 @@ RUN wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_
 
 
 # --- Final image ---
-FROM ubuntu:18.04 as final
+FROM ubuntu:20.04 as final
 
 COPY ./files/common_cleanup.sh /usr/bin/common_cleanup.sh
 
 # Base dependencies
-RUN apt update && apt install --no-install-recommends ca-certificates squashfs-tools -y \
+RUN apt update && apt install --no-install-recommends ca-certificates python3-distutils squashfs-tools -y \
     && /usr/bin/common_cleanup.sh
 
 # Install Docker
diff --git a/compose/base_config.yml b/compose/base_config.yml
index cc2970901..46f37dc7c 100644
--- a/compose/base_config.yml
+++ b/compose/base_config.yml
@@ -9,11 +9,10 @@ galaxy_uwsgi:
   master: false
   virtualenv: .venv
   pythonpath: lib
-  thunder-lock: false
+  thunder-lock: true
   die-on-term: true
   hook-master-start: unix_signal:2 gracefully_kill_them_all
   hook-master-start: unix_signal:15 gracefully_kill_them_all
-  py-call-osafterfork: true
   enable-threads: true
 
 galaxy:
diff --git a/compose/docker-compose.htcondor.yml b/compose/docker-compose.htcondor.yml
index 1b7c36702..35084397f 100644
--- a/compose/docker-compose.htcondor.yml
+++ b/compose/docker-compose.htcondor.yml
@@ -28,6 +28,7 @@ services:
     volumes:
       - ${EXPORT_DIR:-./export}/htcondor:/config
       - ${EXPORT_DIR:-./export}/galaxy/database:/galaxy/database
+      - ${EXPORT_DIR:-./export}/galaxy/lib/galaxy/tools:/galaxy/lib/galaxy/tools:ro
       - ${EXPORT_DIR:-./export}/galaxy/tools:/galaxy/tools:ro
       - ${EXPORT_DIR:-./export}/galaxy/tool-data:/galaxy/tool-data
       - ${EXPORT_DIR:-./export}/galaxy/.venv:/galaxy/.venv
diff --git a/compose/docker-compose.slurm.yml b/compose/docker-compose.slurm.yml
index 134f5e06d..4cf6e29cb 100644
--- a/compose/docker-compose.slurm.yml
+++ b/compose/docker-compose.slurm.yml
@@ -40,6 +40,7 @@ services:
     volumes:
       - ${EXPORT_DIR:-./export}/galaxy/database:/galaxy/database
       - ${EXPORT_DIR:-./export}/galaxy/tools:/galaxy/tools:ro
+      - ${EXPORT_DIR:-./export}/galaxy/lib/galaxy/tools:/galaxy/lib/galaxy/tools:ro
       - ${EXPORT_DIR:-./export}/galaxy/tool-data:/galaxy/tool-data
       - ${EXPORT_DIR:-./export}/galaxy/.venv:/galaxy/.venv
       - ${EXPORT_DIR:-./export}/tool_deps:/tool_deps
diff --git a/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2 b/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2
index 461dfb5ff..9b1ca49ed 100644
--- a/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2
+++ b/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2
@@ -32,6 +32,7 @@
         </destination>
         <destination id="{{ GALAXY_DEPENDENCY_RESOLUTION | default('conda') }}_{{ GALAXY_JOB_RUNNER | default('local') }}" runner="{{ GALAXY_JOB_RUNNER | default('local') }}">
             {% if GALAXY_DEPENDENCY_RESOLUTION == 'singularity' -%}
+              <env file="/galaxy/.venv/bin/activate" />
               <env id="HOME">/home/galaxy</env>
               <param id="singularity_enabled">true</param>
               {% if GALAXY_JOB_RUNNER == 'local' -%}
@@ -59,7 +60,7 @@
               <param id="docker_repo_default">{{ GALAXY_K8S_DOCKER_REPO_DEFAULT | default('docker.io') }}</param>
               {% if GALAXY_K8S_DOCKER_OWNER_DEFAULT -%}<param id="docker_owner_default">{{ GALAXY_K8S_DOCKER_OWNER_DEFAULT }}</param>{% endif -%}
               <param id="docker_image_default">{{ GALAXY_K8S_DOCKER_IMAGE_DEFAULT | default('ubuntu') }}</param>
-              <param id="docker_tag_default">{{ GALAXY_K8S_DOCKER_TAG_DEFAULT | default('18.04') }}</param>
+              <param id="docker_tag_default">{{ GALAXY_K8S_DOCKER_TAG_DEFAULT | default('20.04') }}</param>
               <param id="docker_enabled">true</param>
             {% endif -%}
         </destination>
diff --git a/compose/galaxy-htcondor/Dockerfile b/compose/galaxy-htcondor/Dockerfile
index d10630bde..ac49a826b 100644
--- a/compose/galaxy-htcondor/Dockerfile
+++ b/compose/galaxy-htcondor/Dockerfile
@@ -2,9 +2,9 @@ ARG DOCKER_REGISTRY=quay.io
 ARG DOCKER_REGISTRY_USERNAME=bgruening
 ARG IMAGE_TAG=latest
 
-FROM buildpack-deps:18.04 as galaxy_dependencies
+FROM buildpack-deps:20.04 as galaxy_dependencies
 
-ARG GALAXY_RELEASE=release_20.05
+ARG GALAXY_RELEASE=release_20.09
 ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy
 
 ENV GALAXY_ROOT=/galaxy
@@ -18,7 +18,7 @@ RUN mkdir "${GALAXY_ROOT}" \
     && cd $GALAXY_ROOT/lib \
     && ls . | grep -v "galaxy\|galaxy_ext" | xargs rm -rf \
     && cd $GALAXY_ROOT/lib/galaxy \
-    && ls . | grep -v "__init__.py\|datatypes\|exceptions\|metadata\|model\|util\|security" | xargs rm -rf
+    && ls . | grep -v "__init__.py\|datatypes\|exceptions\|files\|metadata\|model\|util\|security" | xargs rm -rf
 
 
 FROM $DOCKER_REGISTRY/$DOCKER_REGISTRY_USERNAME/galaxy-container-base:$IMAGE_TAG as final
@@ -67,4 +67,6 @@ COPY --chown=$GALAXY_USER:$GALAXY_USER --from=galaxy_dependencies $GALAXY_ROOT $
 COPY start.sh /usr/bin/start.sh
 RUN apt update && apt install python3 -y
 
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 9 
+
 ENTRYPOINT /usr/bin/start.sh
diff --git a/compose/galaxy-server/Dockerfile b/compose/galaxy-server/Dockerfile
index 2245216ec..d789c2250 100644
--- a/compose/galaxy-server/Dockerfile
+++ b/compose/galaxy-server/Dockerfile
@@ -2,7 +2,7 @@ ARG DOCKER_REGISTRY=quay.io
 ARG DOCKER_REGISTRY_USERNAME=bgruening
 ARG IMAGE_TAG=latest
 
-FROM buildpack-deps:18.04 as build_base
+FROM buildpack-deps:20.04 as build_base
 
 ENV EXPORT_DIR=/export \
     GALAXY_ROOT=/galaxy \
@@ -24,7 +24,7 @@ ENV GALAXY_USER=galaxy \
     GALAXY_HOME=/home/galaxy
 
 ENV GALAXY_CONDA_PREFIX=$GALAXY_CONFIG_TOOL_DEPENDENCY_DIR/_conda \
-    MINICONDA_VERSION=4.7.10
+    MINICONDA_VERSION=py38_4.9.2
 
 RUN groupadd -r $GALAXY_USER -g $GALAXY_GID \
     && useradd -u $GALAXY_UID -r -g $GALAXY_USER -d $GALAXY_HOME -c "Galaxy user" --shell /bin/bash $GALAXY_USER \
@@ -34,7 +34,7 @@ RUN groupadd -r $GALAXY_USER -g $GALAXY_GID \
 FROM build_base as build_miniconda
 COPY ./files/common_cleanup.sh /usr/bin/common_cleanup.sh
 # Install Miniconda
-RUN curl -s -L "https://repo.anaconda.com/miniconda/Miniconda2-${MINICONDA_VERSION}-Linux-x86_64.sh" > ~/miniconda.sh \
+RUN curl -s -L "https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" > ~/miniconda.sh \
     && /bin/bash ~/miniconda.sh -b -p $GALAXY_CONDA_PREFIX \
     && rm ~/miniconda.sh \
     && ln -s $GALAXY_CONDA_PREFIX/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
@@ -50,18 +50,20 @@ RUN curl -s -L "https://repo.anaconda.com/miniconda/Miniconda2-${MINICONDA_VERSI
 
 FROM build_base as build_galaxy
 
-ARG GALAXY_RELEASE=release_20.05
+ARG GALAXY_RELEASE=release_20.09
 ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy
 
 COPY ./files/common_cleanup.sh /usr/bin/common_cleanup.sh
 # Install Galaxy
 RUN apt update && apt install --no-install-recommends libcurl4-openssl-dev libssl-dev python3-dev python3-pip -y \
+    && update-alternatives --install /usr/bin/python python /usr/bin/python3 9 \
     && mkdir "${GALAXY_ROOT}" \
     && curl -L -s $GALAXY_REPO/archive/$GALAXY_RELEASE.tar.gz | tar xzf - --strip-components=1 -C $GALAXY_ROOT \
     && cd $GALAXY_ROOT \
     && ./scripts/common_startup.sh \
     && . $GALAXY_ROOT/.venv/bin/activate \
     && pip3 install drmaa psycopg2 pycurl pykube \
+    && pip3 install importlib-metadata importlib-resources pathlib2 ruamel.yaml.clib typing zipp \
     && deactivate \
     && rm -rf .ci .circleci .coveragerc .gitignore .travis.yml CITATION CODE_OF_CONDUCT.md CONTRIBUTING.md CONTRIBUTORS.md \
               LICENSE.txt Makefile README.rst SECURITY_POLICY.md pytest.ini tox.ini \
@@ -73,9 +75,6 @@ RUN apt update && apt install --no-install-recommends libcurl4-openssl-dev libss
 # --- Final image ---
 FROM $DOCKER_REGISTRY/$DOCKER_REGISTRY_USERNAME/galaxy-cluster-base:$IMAGE_TAG as final
 
-ARG GALAXY_RELEASE=release_20.05
-ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy
-
 COPY ./files/common_cleanup.sh /usr/bin/common_cleanup.sh
 COPY ./files/create_galaxy_user.py /usr/local/bin/create_galaxy_user.py
 
@@ -84,7 +83,9 @@ ENV EXPORT_DIR=/export \
     GALAXY_PYTHON=/usr/bin/python3 \
     HTCONDOR_ROOT=/opt/htcondor
 
-ENV GALAXY_STATIC_DIR=$GALAXY_ROOT/static \
+ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_20.09} \
+    GALAXY_REPO=${GALAXY_REPO:-https://github.com/galaxyproject/galaxy} \
+    GALAXY_STATIC_DIR=$GALAXY_ROOT/static \
     GALAXY_EXPORT=$EXPORT_DIR/galaxy \
     GALAXY_CONFIG_DIR=$GALAXY_ROOT/config \
     GALAXY_CONFIG_TOOL_DEPENDENCY_DIR=/tool_deps \
@@ -120,8 +121,7 @@ RUN apt update && apt install --no-install-recommends curl gcc gnupg2 libgomp1 l
 RUN usermod -aG docker $GALAXY_USER
 
 # Make Python3 standard
-RUN mv /usr/bin/python /usr/bin/python2 \
-    && ln /usr/bin/python3 /usr/bin/python
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 9 
 
 COPY --chown=$GALAXY_USER:$GALAXY_USER --from=build_galaxy ${GALAXY_ROOT} ${GALAXY_ROOT}
 COPY --chown=$GALAXY_USER:$GALAXY_USER --from=build_miniconda ${GALAXY_CONFIG_TOOL_DEPENDENCY_DIR} ${GALAXY_CONFIG_TOOL_DEPENDENCY_DIR}
diff --git a/compose/galaxy-server/files/start.sh b/compose/galaxy-server/files/start.sh
index baf672165..860280856 100755
--- a/compose/galaxy-server/files/start.sh
+++ b/compose/galaxy-server/files/start.sh
@@ -13,6 +13,14 @@ create_user() {
   deactivate
 }
 
+# start copy lib/tools. Looks very hacky.
+tools_dir="/galaxy/lib/galaxy/tools/"
+exp_dir="/export$tools_dir"
+mkdir -p $exp_dir
+chown "$GALAXY_USER:$GALAXY_USER" $exp_dir
+cp -rf $tools_dir/* $exp_dir
+# end copy lib/tools.
+
 # First start?? Check if something exists that indicates that environment is not new.. Config file? Something in DB maybe??
 
 echo "Initialization: Check if files already exist, export otherwise."
diff --git a/compose/galaxy-slurm/Dockerfile b/compose/galaxy-slurm/Dockerfile
index 2f1328e8c..6f54338b2 100644
--- a/compose/galaxy-slurm/Dockerfile
+++ b/compose/galaxy-slurm/Dockerfile
@@ -2,9 +2,9 @@ ARG DOCKER_REGISTRY=quay.io
 ARG DOCKER_REGISTRY_USERNAME=bgruening
 ARG IMAGE_TAG=latest
 
-FROM buildpack-deps:18.04 as galaxy_dependencies
+FROM buildpack-deps:20.04 as galaxy_dependencies
 
-ARG GALAXY_RELEASE=release_20.05
+ARG GALAXY_RELEASE=release_20.09
 ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy
 
 ENV GALAXY_ROOT=/galaxy
@@ -17,7 +17,7 @@ RUN mkdir "${GALAXY_ROOT}" \
     && cd $GALAXY_ROOT/lib \
     && ls . | grep -v "galaxy\|galaxy_ext" | xargs rm -rf \
     && cd $GALAXY_ROOT/lib/galaxy \
-    && ls . | grep -v "__init__.py\|datatypes\|exceptions\|metadata\|model\|util\|security" | xargs rm -rf
+    && ls . | grep -v "__init__.py\|datatypes\|exceptions\|files\|metadata\|model\|util\|security" | xargs rm -rf
 
 
 FROM $DOCKER_REGISTRY/$DOCKER_REGISTRY_USERNAME/galaxy-container-base:$IMAGE_TAG as final
@@ -45,11 +45,13 @@ ENV SLURM_USER=galaxy \
 RUN groupadd -r $MUNGER_USER -g $MUNGE_GID \
     && useradd -u $MUNGE_UID -r -g $MUNGER_USER $MUNGER_USER \
     && apt update \
-    && apt install --no-install-recommends gosu munge python python-dev slurm-wlm -y \
+    && apt install --no-install-recommends gosu munge python3 python3-dev slurm-wlm -y \
     && rm -rf /var/lib/apt/lists/* && rm -rf /var/cache/* && find / -name '*.pyc' -delete
 
 # Copy Galaxy dependencies
 COPY --chown=$GALAXY_USER:$GALAXY_USER --from=galaxy_dependencies $GALAXY_ROOT $GALAXY_ROOT
+# Make Python3 standard
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 9 
 
 COPY start.sh /usr/bin/start.sh
 
diff --git a/compose/pulsar/Dockerfile b/compose/pulsar/Dockerfile
index 2fb2a7d10..dac9b1503 100644
--- a/compose/pulsar/Dockerfile
+++ b/compose/pulsar/Dockerfile
@@ -2,9 +2,9 @@ ARG DOCKER_REGISTRY=quay.io
 ARG DOCKER_REGISTRY_USERNAME=bgruening
 ARG IMAGE_TAG=latest
 
-FROM buildpack-deps:18.04 as build_pulsar
+FROM buildpack-deps:20.04 as build_pulsar
 
-ARG PULSAR_RELEASE=0.13.0
+ARG PULSAR_RELEASE=0.14.0
 ARG PULSAR_REPO=https://github.com/galaxyproject/pulsar
 
 ENV PULSAR_ROOT=/pulsar
@@ -34,7 +34,7 @@ ENV PULSAR_VIRTUALENV=$PULSAR_ROOT/.venv \
     PULSAR_TOOL_DEPENDENCY_DIR=$PULSAR_ROOT/dependencies
 
 RUN apt update \
-    && apt install --no-install-recommends ca-certificates curl libxml2-dev libpython3.6 python3 -y \
+    && apt install --no-install-recommends ca-certificates curl libxml2-dev python3 -y \
     && /usr/bin/common_cleanup.sh
 
 COPY --from=build_pulsar /pulsar /pulsar
diff --git a/compose/tests/docker-compose.test.bioblend.yml b/compose/tests/docker-compose.test.bioblend.yml
index 9ebcaf7b8..6b77fb405 100644
--- a/compose/tests/docker-compose.test.bioblend.yml
+++ b/compose/tests/docker-compose.test.bioblend.yml
@@ -4,7 +4,7 @@ services:
     image: ${DOCKER_REGISTRY:-quay.io}/${DOCKER_REGISTRY_USERNAME:-bgruening}/galaxy-bioblend-test:${IMAGE_TAG:-latest}
     build: tests/galaxy-bioblend-test
     environment:
-      - GALAXY_VERSION=${GALAXY_VERSION:-release_20.05} # TODO: Change to GALAXY_RELEASE
+      - GALAXY_VERSION=${GALAXY_VERSION:-release_20.09} # TODO: Change to GALAXY_RELEASE
       - GALAXY_URL=http://nginx${GALAXY_PROXY_PREFIX:-}/
     networks:
       - galaxy
diff --git a/compose/tests/galaxy-selenium-test/Dockerfile b/compose/tests/galaxy-selenium-test/Dockerfile
index f081a029e..370264852 100644
--- a/compose/tests/galaxy-selenium-test/Dockerfile
+++ b/compose/tests/galaxy-selenium-test/Dockerfile
@@ -1,18 +1,19 @@
 FROM selenium/standalone-chrome:3.141.59
 
-ARG GALAXY_RELEASE=release_20.05
+ARG GALAXY_RELEASE=release_20.09
 ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy
 
 ENV GALAXY_ROOT=/galaxy
-ENV GALAXY_PYTHON=/usr/bin/python
+ENV GALAXY_PYTHON=/usr/bin/python3
 
 USER root
-RUN apt update && apt install --no-install-recommends python-dev python-pip -y && rm -rf /var/lib/apt/lists/* \
+RUN apt update && apt install --no-install-recommends python3-dev python3-pip -y && rm -rf /var/lib/apt/lists/* \
     && mkdir "${GALAXY_ROOT}" \
     && chown seluser "${GALAXY_ROOT}"
 
 USER seluser
-RUN curl -L -s $GALAXY_REPO/archive/$GALAXY_RELEASE.tar.gz | tar xzf - --strip-components=1 -C $GALAXY_ROOT \
+RUN mkdir -p $GALAXY_ROOT && \
+    curl -L -s $GALAXY_REPO/archive/$GALAXY_RELEASE.tar.gz | tar xzf - --strip-components=1 -C $GALAXY_ROOT \
     && cd "${GALAXY_ROOT}" \
     && ./scripts/common_startup.sh --skip-client-build --dev-wheels
 
diff --git a/compose/tests/galaxy-workflow-test/Dockerfile b/compose/tests/galaxy-workflow-test/Dockerfile
index b392babbb..1b9385da9 100644
--- a/compose/tests/galaxy-workflow-test/Dockerfile
+++ b/compose/tests/galaxy-workflow-test/Dockerfile
@@ -1,7 +1,7 @@
 FROM alpine:3.11
 
-ENV TEST_REPO=${TEST_REPO:-https://github.com/usegalaxy-eu/workflow-testing} \
-    TEST_RELEASE=${TEST_RELEASE:-master}
+ENV TEST_REPO=${TEST_REPO:-https://github.com/jonas27/workflow-testing} \
+    TEST_RELEASE=${TEST_RELEASE:-20.09-comment-filetype}
 
 RUN apk add --no-cache bash python3 curl \
     && apk add --no-cache --virtual build-dep gcc libxml2-dev libxslt-dev musl-dev linux-headers python3-dev \
@@ -10,6 +10,9 @@ RUN apk add --no-cache bash python3 curl \
     && curl -L -s $TEST_REPO/archive/$TEST_RELEASE.tar.gz | tar xzf - --strip-components=1 \
     && apk del build-dep
 
+# Make Python3 standard
+RUN ln /usr/bin/python3 /usr/bin/python && ln /usr/bin/python3 /usr/bin/python2
+
 ADD ./run.sh /usr/bin/run.sh
 
 WORKDIR /src
diff --git a/galaxy/Dockerfile b/galaxy/Dockerfile
index 2b46ec66c..ffe96856e 100644
--- a/galaxy/Dockerfile
+++ b/galaxy/Dockerfile
@@ -16,60 +16,60 @@ MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com
 ARG GALAXY_RELEASE
 ARG GALAXY_REPO
 
-ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_20.05} \
-GALAXY_REPO=${GALAXY_REPO:-https://github.com/galaxyproject/galaxy} \
-GALAXY_ROOT=/galaxy-central \
-GALAXY_CONFIG_DIR=/etc/galaxy \
-EXPORT_DIR=/export \
-DEBIAN_FRONTEND=noninteractive \
-PG_VERSION=11
-
+ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_20.09} \
+    GALAXY_REPO=${GALAXY_REPO:-https://github.com/galaxyproject/galaxy} \
+    GALAXY_ROOT=/galaxy-central \
+    GALAXY_CONFIG_DIR=/etc/galaxy \
+    EXPORT_DIR=/export \
+    DEBIAN_FRONTEND=noninteractive \
+    PG_VERSION=11
 
 ENV GALAXY_CONFIG_FILE=$GALAXY_CONFIG_DIR/galaxy.yml \
-GALAXY_CONFIG_JOB_CONFIG_FILE=$GALAXY_CONFIG_DIR/job_conf.xml \
-GALAXY_CONFIG_JOB_METRICS_CONFIG_FILE=$GALAXY_CONFIG_DIR/job_metrics_conf.xml \
-GALAXY_CONFIG_TOOL_DATA_TABLE_CONFIG_PATH=/etc/galaxy/tool_data_table_conf.xml \
-GALAXY_CONFIG_WATCH_TOOL_DATA_DIR=True \
-GALAXY_CONFIG_TOOL_DEPENDENCY_DIR=$EXPORT_DIR/tool_deps \
-GALAXY_CONFIG_TOOL_PATH=$EXPORT_DIR/galaxy-central/tools \
-GALAXY_VIRTUAL_ENV=/galaxy_venv \
-GALAXY_USER=galaxy \
-GALAXY_UID=1450 \
-GALAXY_GID=1450 \
-GALAXY_POSTGRES_UID=1550 \
-GALAXY_POSTGRES_GID=1550 \
-GALAXY_HOME=/home/galaxy \
-GALAXY_LOGS_DIR=/home/galaxy/logs \
-GALAXY_DEFAULT_ADMIN_USER=admin \
-GALAXY_DEFAULT_ADMIN_EMAIL=admin@galaxy.org \
-GALAXY_DEFAULT_ADMIN_PASSWORD=password \
-GALAXY_DEFAULT_ADMIN_KEY=fakekey \
-GALAXY_DESTINATIONS_DEFAULT=slurm_cluster \
-GALAXY_RUNNERS_ENABLE_SLURM=True \
-GALAXY_RUNNERS_ENABLE_CONDOR=False \
-GALAXY_CONFIG_DATABASE_CONNECTION=postgresql://galaxy:galaxy@localhost:5432/galaxy?client_encoding=utf8 \
-GALAXY_CONFIG_ADMIN_USERS=admin@galaxy.org \
-GALAXY_CONFIG_MASTER_API_KEY=HSNiugRFvgT574F43jZ7N9F3 \
-GALAXY_CONFIG_BRAND="Galaxy Docker Build" \
-GALAXY_CONFIG_STATIC_ENABLED=False \
-# Define the default postgresql database path
-PG_DATA_DIR_DEFAULT=/var/lib/postgresql/$PG_VERSION/main/ \
-PG_CONF_DIR_DEFAULT=/etc/postgresql/$PG_VERSION/main/ \
-PG_DATA_DIR_HOST=$EXPORT_DIR/postgresql/$PG_VERSION/main/ \
-# The following 2 ENV vars can be used to set the number of uwsgi processes and threads
-UWSGI_PROCESSES=2 \
-UWSGI_THREADS=4 \
-# Set HTTPS to use a self-signed certificate (or your own certificate in $EXPORT_DIR/{server.key,server.crt})
-USE_HTTPS=False \
-# Set USE_HTTPS_LENSENCRYPT and GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL to a domain that is reachable to get a letsencrypt certificate
-USE_HTTPS_LETSENCRYPT=False \
-GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL=http://localhost \
-# Set the number of Galaxy handlers
-GALAXY_HANDLER_NUMPROCS=2 \
-# Setting a standard encoding. This can get important for things like the unix sort tool.
-LC_ALL=en_US.UTF-8 \
-LANG=en_US.UTF-8 \
-GALAXY_CONDA_PREFIX=/tool_deps/_conda
+    GALAXY_CONFIG_JOB_CONFIG_FILE=$GALAXY_CONFIG_DIR/job_conf.xml \
+    GALAXY_CONFIG_JOB_METRICS_CONFIG_FILE=$GALAXY_CONFIG_DIR/job_metrics_conf.xml \
+    GALAXY_CONFIG_TOOL_DATA_TABLE_CONFIG_PATH=/etc/galaxy/tool_data_table_conf.xml \
+    GALAXY_CONFIG_WATCH_TOOL_DATA_DIR=True \
+    GALAXY_CONFIG_TOOL_DEPENDENCY_DIR=$EXPORT_DIR/tool_deps \
+    GALAXY_CONFIG_TOOL_PATH=$EXPORT_DIR/galaxy-central/tools \
+    GALAXY_VIRTUAL_ENV=/galaxy_venv \
+    GALAXY_USER=galaxy \
+    GALAXY_UID=1450 \
+    GALAXY_GID=1450 \
+    GALAXY_POSTGRES_UID=1550 \
+    GALAXY_POSTGRES_GID=1550 \
+    GALAXY_HOME=/home/galaxy \
+    GALAXY_LOGS_DIR=/home/galaxy/logs \
+    GALAXY_DEFAULT_ADMIN_USER=admin \
+    GALAXY_DEFAULT_ADMIN_EMAIL=admin@galaxy.org \
+    GALAXY_DEFAULT_ADMIN_PASSWORD=password \
+    GALAXY_DEFAULT_ADMIN_KEY=fakekey \
+    GALAXY_DESTINATIONS_DEFAULT=slurm_cluster \
+    GALAXY_RUNNERS_ENABLE_SLURM=True \
+    GALAXY_RUNNERS_ENABLE_CONDOR=False \
+    GALAXY_CONFIG_DATABASE_CONNECTION=postgresql://galaxy:galaxy@localhost:5432/galaxy?client_encoding=utf8 \
+    GALAXY_CONFIG_ADMIN_USERS=admin@galaxy.org \
+    GALAXY_CONFIG_MASTER_API_KEY=HSNiugRFvgT574F43jZ7N9F3 \
+    GALAXY_CONFIG_BRAND="Galaxy Docker Build" \
+    GALAXY_CONFIG_STATIC_ENABLED=False \
+    # Define the default postgresql database path
+    PG_DATA_DIR_DEFAULT=/var/lib/postgresql/$PG_VERSION/main/ \
+    PG_CONF_DIR_DEFAULT=/etc/postgresql/$PG_VERSION/main/ \
+    PG_DATA_DIR_HOST=$EXPORT_DIR/postgresql/$PG_VERSION/main/ \
+    # The following 2 ENV vars can be used to set the number of uwsgi processes and threads
+    UWSGI_PROCESSES=2 \
+    UWSGI_THREADS=4 \
+    # Set HTTPS to use a self-signed certificate (or your own certificate in $EXPORT_DIR/{server.key,server.crt})
+    USE_HTTPS=False \
+    # Set USE_HTTPS_LENSENCRYPT and GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL to a domain that is reachable to get a letsencrypt certificate
+    USE_HTTPS_LETSENCRYPT=False \
+    GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL=http://localhost \
+    # Set the number of Galaxy handlers
+    GALAXY_HANDLER_NUMPROCS=2 \
+    # Setting a standard encoding. This can get important for things like the unix sort tool.
+    LC_ALL=en_US.UTF-8 \
+    LANG=en_US.UTF-8 \
+    NODE_OPTIONS=--max-old-space-size=4096 \
+    GALAXY_CONDA_PREFIX=/tool_deps/_conda
 
 # 16MB
 RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup \
@@ -118,7 +118,7 @@ ADD ./bashrc $GALAXY_HOME/.bashrc
 # Install miniconda, then virtualenv from conda and then
 # download latest stable release of Galaxy.
 
-RUN curl -s -L https://repo.continuum.io/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh > ~/miniconda.sh \
+RUN curl -s -L https://repo.anaconda.com/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh > ~/miniconda.sh \
     && /bin/bash ~/miniconda.sh -b -p $GALAXY_CONDA_PREFIX/ \
     && rm ~/miniconda.sh \
     && ln -s $GALAXY_CONDA_PREFIX/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
@@ -188,30 +188,35 @@ RUN mkdir -p /shed_tools $EXPORT_DIR/ftp/ \
     && chown $GALAXY_USER:$GALAXY_USER $EXPORT_DIR/tool_deps \
     && apt update -qq && apt install --no-install-recommends -y ansible \
     && ansible-playbook /ansible/provision.yml \
-        --extra-vars galaxy_venv_dir=$GALAXY_VIRTUAL_ENV \
-        --extra-vars galaxy_log_dir=$GALAXY_LOGS_DIR \
-        --extra-vars galaxy_user_name=$GALAXY_USER \
-        --extra-vars galaxy_config_file=$GALAXY_CONFIG_FILE \
-        --extra-vars galaxy_config_dir=$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 galaxy_extras_config_condor=True \
-        --extra-vars galaxy_extras_config_condor_docker=True \
-        --extra-vars galaxy_extras_config_rabbitmq=True \
-        --extra-vars galaxy_extras_config_cvmfs=True \
-        --extra-vars galaxy_extras_config_uwsgi=False \
-        --extra-vars proftpd_db_connection=galaxy@galaxy \
-        --extra-vars proftpd_files_dir=$EXPORT_DIR/ftp \
-        --extra-vars proftpd_use_sftp=True \
-        --extra-vars galaxy_extras_docker_legacy=False \
-        --extra-vars galaxy_minimum_version=19.01 \
-        --extra-vars supervisor_postgres_config_path=$PG_CONF_DIR_DEFAULT/postgresql.conf \
-        --extra-vars supervisor_postgres_autostart=false \
-        --extra-vars nginx_use_remote_header=True \
-        --tags=galaxyextras,cvmfs -c local \
+    --extra-vars galaxy_venv_dir=$GALAXY_VIRTUAL_ENV \
+    --extra-vars galaxy_log_dir=$GALAXY_LOGS_DIR \
+    --extra-vars galaxy_user_name=$GALAXY_USER \
+    --extra-vars galaxy_config_file=$GALAXY_CONFIG_FILE \
+    --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=$GALAXY_CONFIG_JOB_METRICS_CONFIG_FILE \
+    --extra-vars supervisor_manage_slurm="" \
+    --extra-vars galaxy_extras_config_condor=True \
+    --extra-vars galaxy_extras_config_condor_docker=True \
+    --extra-vars galaxy_extras_config_rabbitmq=True \
+    --extra-vars galaxy_extras_config_cvmfs=True \
+    --extra-vars galaxy_extras_config_uwsgi=False \
+    --extra-vars proftpd_db_connection=galaxy@galaxy \
+    --extra-vars proftpd_files_dir=$EXPORT_DIR/ftp \
+    --extra-vars proftpd_use_sftp=True \
+    --extra-vars galaxy_extras_docker_legacy=False \
+    --extra-vars galaxy_minimum_version=19.01 \
+    --extra-vars supervisor_postgres_config_path=$PG_CONF_DIR_DEFAULT/postgresql.conf \
+    --extra-vars supervisor_postgres_autostart=false \
+    --extra-vars nginx_use_remote_header=True \
+    --tags=galaxyextras,cvmfs -c local \
+    && . $GALAXY_VIRTUAL_ENV/bin/activate \
+    && pip install WeasyPrint \
+    && deactivate \
     # TODO: no clue why this is needed here again
     && cd $GALAXY_ROOT && ./scripts/common_startup.sh \
+    && cd config && find . -name 'node_modules' -type d -prune -exec rm -rf '{}' + \
+    && find . -name '.cache' -type d -prune -exec rm -rf '{}' + \
     && cd / \
     && rm $PG_DATA_DIR_DEFAULT -rf \
     && python /usr/local/bin/setup_postgresql.py --dbuser galaxy --dbpassword galaxy --db-name galaxy --dbpath $PG_DATA_DIR_DEFAULT --dbversion $PG_VERSION \
@@ -238,28 +243,28 @@ WORKDIR $GALAXY_ROOT
 #RUN export GALAXY=$GALAXY_ROOT && sh ./cron/updateucsc.sh.sample
 
 ENV GALAXY_CONFIG_JOB_WORKING_DIRECTORY=$EXPORT_DIR/galaxy-central/database/job_working_directory \
-GALAXY_CONFIG_FILE_PATH=$EXPORT_DIR/galaxy-central/database/files \
-GALAXY_CONFIG_NEW_FILE_PATH=$EXPORT_DIR/galaxy-central/database/files \
-GALAXY_CONFIG_TEMPLATE_CACHE_PATH=$EXPORT_DIR/galaxy-central/database/compiled_templates \
-GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=$EXPORT_DIR/galaxy-central/database/citations/data \
-GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=$EXPORT_DIR/galaxy-central/database/pbs \
-GALAXY_CONFIG_FTP_UPLOAD_DIR=$EXPORT_DIR/ftp \
-GALAXY_CONFIG_FTP_UPLOAD_SITE=galaxy.docker.org \
-GALAXY_CONFIG_USE_PBKDF2=False \
-GALAXY_CONFIG_NGINX_X_ACCEL_REDIRECT_BASE=/_x_accel_redirect \
-GALAXY_CONFIG_NGINX_X_ARCHIVE_FILES_BASE=/_x_accel_redirect \
-GALAXY_CONFIG_DYNAMIC_PROXY_MANAGE=False \
-GALAXY_CONFIG_VISUALIZATION_PLUGINS_DIRECTORY=config/plugins/visualizations \
-GALAXY_CONFIG_TRUST_IPYTHON_NOTEBOOK_CONVERSION=True \
-GALAXY_CONFIG_TOOLFORM_UPGRADE=True \
-GALAXY_CONFIG_SANITIZE_ALL_HTML=False \
-GALAXY_CONFIG_TOOLFORM_UPGRADE=True \
-GALAXY_CONFIG_WELCOME_URL=$GALAXY_CONFIG_DIR/web/welcome.html \
-GALAXY_CONFIG_OVERRIDE_DEBUG=False \
-GALAXY_CONFIG_ENABLE_QUOTAS=True \
-# We need to set $HOME for some Tool Shed tools (e.g Perl libs with $HOME/.cpan)
-HOME=$GALAXY_HOME \
-GALAXY_CONDA_PREFIX=$GALAXY_CONFIG_TOOL_DEPENDENCY_DIR/_conda
+    GALAXY_CONFIG_FILE_PATH=$EXPORT_DIR/galaxy-central/database/files \
+    GALAXY_CONFIG_NEW_FILE_PATH=$EXPORT_DIR/galaxy-central/database/files \
+    GALAXY_CONFIG_TEMPLATE_CACHE_PATH=$EXPORT_DIR/galaxy-central/database/compiled_templates \
+    GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=$EXPORT_DIR/galaxy-central/database/citations/data \
+    GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=$EXPORT_DIR/galaxy-central/database/pbs \
+    GALAXY_CONFIG_FTP_UPLOAD_DIR=$EXPORT_DIR/ftp \
+    GALAXY_CONFIG_FTP_UPLOAD_SITE=galaxy.docker.org \
+    GALAXY_CONFIG_USE_PBKDF2=False \
+    GALAXY_CONFIG_NGINX_X_ACCEL_REDIRECT_BASE=/_x_accel_redirect \
+    GALAXY_CONFIG_NGINX_X_ARCHIVE_FILES_BASE=/_x_accel_redirect \
+    GALAXY_CONFIG_DYNAMIC_PROXY_MANAGE=False \
+    GALAXY_CONFIG_VISUALIZATION_PLUGINS_DIRECTORY=config/plugins/visualizations \
+    GALAXY_CONFIG_TRUST_IPYTHON_NOTEBOOK_CONVERSION=True \
+    GALAXY_CONFIG_TOOLFORM_UPGRADE=True \
+    GALAXY_CONFIG_SANITIZE_ALL_HTML=False \
+    GALAXY_CONFIG_TOOLFORM_UPGRADE=True \
+    GALAXY_CONFIG_WELCOME_URL=$GALAXY_CONFIG_DIR/web/welcome.html \
+    GALAXY_CONFIG_OVERRIDE_DEBUG=False \
+    GALAXY_CONFIG_ENABLE_QUOTAS=True \
+    # We need to set $HOME for some Tool Shed tools (e.g Perl libs with $HOME/.cpan)
+    HOME=$GALAXY_HOME \
+    GALAXY_CONDA_PREFIX=$GALAXY_CONFIG_TOOL_DEPENDENCY_DIR/_conda
 
 # Container Style
 ADD GalaxyDocker.png $GALAXY_CONFIG_DIR/web/welcome_image.png
@@ -276,10 +281,10 @@ ADD welcome.html $GALAXY_CONFIG_DIR/web/welcome.html
 #    && find $GALAXY_VIRTUAL_ENV -name '*.pyc' -delete \
 #    && rm -rf /tmp/* $GALAXY_ROOT/client/node_modules/ $GALAXY_VIRTUAL_ENV/src/ /home/galaxy/.cache/ /home/galaxy/.npm
 
-    # Install all required Node dependencies. This is required to get proxy support to work for Interactive Environments
-    #cd $GALAXY_ROOT/lib/galaxy/web/proxy/js && \
-    #npm install && \
-    #rm -rf ~/.cache/ $GALAXY_ROOT/client/node_modules/
+# Install all required Node dependencies. This is required to get proxy support to work for Interactive Environments
+#cd $GALAXY_ROOT/lib/galaxy/web/proxy/js && \
+#npm install && \
+#rm -rf ~/.cache/ $GALAXY_ROOT/client/node_modules/
 
 # Switch back to User root
 USER root
@@ -304,6 +309,10 @@ RUN echo "DISCARD_SESSION_KEYRING_ON_STARTUP=False" > /etc/condor/condor_config.
 ADD https://github.com/krallin/tini/releases/download/v0.18.0/tini /sbin/tini
 RUN chmod +x /sbin/tini
 
+# https://stackoverflow.com/questions/62250160/uwsgi-runtimeerror-cannot-release-un-acquired-lock
+ADD run.sh $GALAXY_ROOT/run.sh
+RUN chmod +x $GALAXY_ROOT/run.sh && sed -i 's/py-call-osafterfork.*//g' /etc/galaxy/galaxy.yml
+
 # This needs to happen here and not above, otherwise the Galaxy start
 # (without running the startup.sh script) will crash because integrated_tool_panel.xml could not be found.
 ENV GALAXY_CONFIG_INTEGRATED_TOOL_PANEL_CONFIG $EXPORT_DIR/galaxy-central/integrated_tool_panel.xml
diff --git a/galaxy/roles/galaxy-postgresql b/galaxy/roles/galaxy-postgresql
index f363e42e3..1507fbe5e 160000
--- a/galaxy/roles/galaxy-postgresql
+++ b/galaxy/roles/galaxy-postgresql
@@ -1 +1 @@
-Subproject commit f363e42e373dce38e8dceb75acb07e770f71b83c
+Subproject commit 1507fbe5eda946fc9f4c9aabef4e73a9b11a8315
diff --git a/galaxy/roles/galaxyprojectdotorg.galaxyextras b/galaxy/roles/galaxyprojectdotorg.galaxyextras
index b9e47789f..82da900da 160000
--- a/galaxy/roles/galaxyprojectdotorg.galaxyextras
+++ b/galaxy/roles/galaxyprojectdotorg.galaxyextras
@@ -1 +1 @@
-Subproject commit b9e47789f9b2be2a18d3db3d9585893ddefca062
+Subproject commit 82da900da5667a4d1e06ff976487d30ce460a59d
diff --git a/galaxy/run.sh b/galaxy/run.sh
new file mode 100755
index 000000000..fa54e0f25
--- /dev/null
+++ b/galaxy/run.sh
@@ -0,0 +1,98 @@
+#!/bin/sh
+
+
+# Usage: ./run.sh <start|stop|restart>
+#
+#
+# Description: This script can be used to start or stop the galaxy
+# web application.
+
+cd "$(dirname "$0")"
+
+. ./scripts/common_startup_functions.sh
+
+
+# If there is a file that defines a shell environment specific to this
+# instance of Galaxy, source the file.
+if [ -z "$GALAXY_LOCAL_ENV_FILE" ];
+then
+    GALAXY_LOCAL_ENV_FILE='./config/local_env.sh'
+fi
+
+if [ -f "$GALAXY_LOCAL_ENV_FILE" ];
+then
+    . "$GALAXY_LOCAL_ENV_FILE"
+fi
+
+GALAXY_PID=${GALAXY_PID:-galaxy.pid}
+GALAXY_LOG=${GALAXY_LOG:-galaxy.log}
+PID_FILE=$GALAXY_PID
+LOG_FILE=$GALAXY_LOG
+
+parse_common_args $@
+
+run_common_start_up
+
+setup_python
+
+
+if [ ! -z "$GALAXY_RUN_WITH_TEST_TOOLS" ];
+then
+    export GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE="$(pwd)/test/functional/tools/samples_tool_conf.xml"
+    export GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES="true"
+    export GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_TOOL_FORMATS="true"
+    export GALAXY_CONFIG_INTERACTIVETOOLS_ENABLE="true"
+    export GALAXY_CONFIG_OVERRIDE_WEBHOOKS_DIR="test/functional/webhooks"
+fi
+
+set_galaxy_config_file_var
+
+
+if [ "$INITIALIZE_TOOL_DEPENDENCIES" -eq 1 ]; then
+    # Install Conda environment if needed.
+    python ./scripts/manage_tool_dependencies.py init_if_needed
+fi
+
+[ -n "$GALAXY_UWSGI" ] && APP_WEBSERVER='uwsgi'
+find_server "${GALAXY_CONFIG_FILE:-none}" galaxy
+server_args=`echo $server_args | sed 's/--py-call-osafterfork//g'`
+
+
+if [ "$run_server" = "python" -a -n "$GALAXY_RUN_ALL" ]; then
+    servers=$(sed -n 's/^\[server:\(.*\)\]/\1/  p' "$GALAXY_CONFIG_FILE" | xargs echo)
+    if [ -z "$stop_daemon_arg_set" -a -z "$daemon_or_restart_arg_set" ]; then
+        echo "ERROR: \$GALAXY_RUN_ALL cannot be used without the '--daemon', '--stop-daemon', 'restart', 'start' or 'stop' arguments to run.sh"
+        exit 1
+    fi
+    for server in $servers; do
+        echo "Executing: python $server_args --server-name=\"$server\" --pid-file=\"$server.pid\" --log-file=\"$server.log\""
+        eval python $server_args --server-name="$server" --pid-file="$server.pid" --log-file="$server.log"
+        if [ -n "$wait_arg_set" -a -n "$daemon_or_restart_arg_set" ]; then
+            while true; do
+                sleep 1
+                # Grab the current pid from the pid file and remove any trailing space
+                if ! current_pid_in_file=$(sed -e 's/[[:space:]]*$//' "$server.pid"); then
+                    echo "A Galaxy process died, interrupting" >&2
+                    exit 1
+                fi
+                if [ -n "$current_pid_in_file" ]; then
+                    echo "Found PID $current_pid_in_file in '$server.pid', monitoring '$server.log'"
+                else
+                    echo "No PID found in '$server.pid' yet"
+                    continue
+                fi
+                # Search for all pids in the logs and tail for the last one
+                latest_pid=$(grep '^Starting server in PID [0-9]\+\.$' "$server.log" | sed 's/^Starting server in PID \([0-9]\{1,\}\).$/\1/' | tail -n 1)
+                # If they're equivalent, then the current pid file agrees with our logs
+                # and we've succesfully started
+                [ -n "$latest_pid" ] && [ "$latest_pid" -eq "$current_pid_in_file" ] && break
+            done
+            echo
+        fi
+    done
+else
+
+    echo "Executing: $run_server $server_args"
+    # args are properly quoted so use eval
+    eval $run_server $server_args
+fi
diff --git a/test/slurm/Dockerfile b/test/slurm/Dockerfile
index 76495a16d..bf74cf193 100644
--- a/test/slurm/Dockerfile
+++ b/test/slurm/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:18.04
+FROM ubuntu:20.04
 
 ENV DEBIAN_FRONTEND noninteractive