diff --git a/.github/workflows/compose.yml b/.github/workflows/compose.yml index 2dbf435f6..475bbff93 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 @@ -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 }}" >> $GITHUB_ENV - name: Run tests for the first time if: steps.run_check.outputs.run run: | diff --git a/.github/workflows/pull-request.yml b/.github/workflows/pull-request.yml index 9eb289190..12baa530c 100644 --- a/.github/workflows/pull-request.yml +++ b/.github/workflows/pull-request.yml @@ -2,7 +2,7 @@ name: pr-test on: pull_request jobs: test: - runs-on: ubuntu-latest + runs-on: ubuntu-20.04 strategy: matrix: infrastructure: @@ -30,6 +30,7 @@ jobs: exclude_test: - workflow_example1 - workflow_mapping_by_sequencing + - workflow_ard # - name: galaxy-pulsar-mq # files: -f docker-compose.yml -f docker-compose.pulsar.yml -f docker-compose.pulsar.mq.yml # exclude_test: @@ -41,6 +42,7 @@ jobs: - bioblend - workflow_ard - workflow_mapping_by_sequencing + - workflow_example1 - selenium - name: galaxy-singularity files: -f docker-compose.yml -f docker-compose.singularity.yml @@ -108,7 +110,7 @@ jobs: uses: actions/checkout@v2 - name: Set WORKFLOWS env for worfklows-test if: matrix.test.workflow - run: echo "::set-env name=WORKFLOWS::${{ 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/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 [[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 f3640e038..46f37dc7c 100644 --- a/compose/base_config.yml +++ b/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: 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 - ${EXPORT_DIR:-./export}/tool_deps:/tool_deps diff --git a/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2 b/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2 index 461dfb5ff..9b1ca49ed 100644 --- a/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2 +++ b/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2 @@ -32,6 +32,7 @@ {% if GALAXY_DEPENDENCY_RESOLUTION == 'singularity' -%} + /home/galaxy true {% if GALAXY_JOB_RUNNER == 'local' -%} @@ -59,7 +60,7 @@ {{ GALAXY_K8S_DOCKER_REPO_DEFAULT | default('docker.io') }} {% if GALAXY_K8S_DOCKER_OWNER_DEFAULT -%}{{ GALAXY_K8S_DOCKER_OWNER_DEFAULT }}{% endif -%} {{ GALAXY_K8S_DOCKER_IMAGE_DEFAULT | default('ubuntu') }} - {{ GALAXY_K8S_DOCKER_TAG_DEFAULT | default('18.04') }} + {{ GALAXY_K8S_DOCKER_TAG_DEFAULT | default('20.04') }} true {% endif -%} diff --git a/compose/galaxy-htcondor/Dockerfile b/compose/galaxy-htcondor/Dockerfile index d10630bde..ac49a826b 100644 --- a/compose/galaxy-htcondor/Dockerfile +++ b/compose/galaxy-htcondor/Dockerfile @@ -2,9 +2,9 @@ ARG DOCKER_REGISTRY=quay.io ARG DOCKER_REGISTRY_USERNAME=bgruening ARG IMAGE_TAG=latest -FROM buildpack-deps:18.04 as galaxy_dependencies +FROM buildpack-deps:20.04 as galaxy_dependencies -ARG GALAXY_RELEASE=release_20.05 +ARG GALAXY_RELEASE=release_20.09 ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy ENV GALAXY_ROOT=/galaxy @@ -18,7 +18,7 @@ RUN mkdir "${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 9d4dc8872..d789c2250 100644 --- a/compose/galaxy-server/Dockerfile +++ b/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} ${GALAXY_CONFIG_TOOL_DEPENDENCY_DIR} diff --git a/compose/galaxy-server/files/start.sh b/compose/galaxy-server/files/start.sh index baf672165..860280856 100755 --- a/compose/galaxy-server/files/start.sh +++ b/compose/galaxy-server/files/start.sh @@ -13,6 +13,14 @@ create_user() { deactivate } +# start copy lib/tools. Looks very hacky. +tools_dir="/galaxy/lib/galaxy/tools/" +exp_dir="/export$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 ffe96856e..e2ef0d6ea 100644 --- a/galaxy/Dockerfile +++ b/galaxy/Dockerfile @@ -2,7 +2,7 @@ # # VERSION Galaxy-central -FROM ubuntu:18.04 +FROM ubuntu:20.04 MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com 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