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Merge pull request #569 from bgruening/20.09
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,139 @@ | ||
| #!/bin/bash | ||
| set -ex | ||
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| 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 | ||
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| 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 | ||
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| pip3 install ephemeris | ||
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| docker --version | ||
| docker info | ||
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| # start building this repo | ||
| git submodule update --init --recursive | ||
| sudo chown 1450 /tmp && sudo chmod a=rwx /tmp | ||
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| ## define a container size check function, first parameter is the container name, second the max allowed size in MB | ||
| container_size_check () { | ||
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| # 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. $2" | ||
| sleep 2 | ||
| #exit | ||
| fi | ||
| } | ||
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| export WORKING_DIR=${GITHUB_WORKSPACE:-$PWD} | ||
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| export DOCKER_RUN_CONTAINER="quay.io/bgruening/galaxy" | ||
| SAMPLE_TOOLS=$GALAXY_HOME/ephemeris/sample_tool_list.yaml | ||
| cd "$WORKING_DIR" | ||
| docker build -t quay.io/bgruening/galaxy galaxy/ | ||
| #container_size_check quay.io/bgruening/galaxy 1500 | ||
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| mkdir local_folder | ||
| docker run -d -p 8080:80 -p 8021:21 -p 8022:22 \ | ||
| --name galaxy \ | ||
| --privileged=true \ | ||
| -v "$(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 | ||
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| 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 "$WORKING_DIR" | ||
| docker run "$@" | ||
| } | ||
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| docker ps | ||
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| # Test submitting jobs to an external slurm cluster | ||
| cd "${WORKING_DIR}/test/slurm/" && bash test.sh && cd "$WORKING_DIR" | ||
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| # 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 | ||
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| echo 'Waiting for Galaxy to come up.' | ||
| galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 300 | ||
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| curl -v --fail $BIOBLEND_GALAXY_URL/api/version | ||
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| # 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 | ||
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| docker logs httpstest && docker stop httpstest && docker rm httpstest | ||
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| # 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 | ||
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| # 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" | ||
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| # 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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