Merge pull request #577 from jonas27/20.09

20.09

.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
@@ -232,13 +232,13 @@ 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: |

.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)

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)
 

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:
+

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

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

compose/base_config.yml

@@ -13,7 +13,6 @@ galaxy_uwsgi:
   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:

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

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

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>

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

compose/galaxy-server/Dockerfile

@@ -2,10 +2,7 @@ ARG DOCKER_REGISTRY=quay.io
 ARG DOCKER_REGISTRY_USERNAME=bgruening
 ARG IMAGE_TAG=latest
 
-FROM buildpack-deps:18.04 as build_base
-
-ARG GALAXY_RELEASE=release_20.05
-ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy
+FROM buildpack-deps:20.04 as build_base
 
 ENV EXPORT_DIR=/export \
     GALAXY_ROOT=/galaxy \
@@ -27,7 +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 \
@@ -37,7 +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 $GALAXY_CONDA_PREFIX/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
@@ -52,15 +49,21 @@ RUN curl -s -L "https://repo.anaconda.com/miniconda/Miniconda2-${MINICONDA_VERSI
     && /usr/bin/common_cleanup.sh
 
 FROM build_base as build_galaxy
+
+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 \
@@ -80,7 +83,7 @@ ENV EXPORT_DIR=/export \
     GALAXY_PYTHON=/usr/bin/python3 \
     HTCONDOR_ROOT=/opt/htcondor
 
-ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_20.05} \
+ENV GALAXY_RELEASE=${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 \
@@ -118,8 +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}

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."

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
 

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

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