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Merged
merged 5 commits into from
Nov 12, 2024
Merged

bump to 24.1 - Compose setup #608

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112d862
bump to 24.1
jyotipm29 Oct 30, 2024
130be06
added rustus service
jyotipm29 Oct 30, 2024
148dfca
install conda from conda-forge (miniforge)
jyotipm29 Nov 12, 2024
c5c515b
Merge branch 'master' into 24.1-compose
jyotipm29 Nov 12, 2024
4fd2351
fix ubuntu version
jyotipm29 Nov 12, 2024
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115 changes: 50 additions & 65 deletions .github/workflows/compose.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,25 +3,25 @@ on: [push]
jobs:
build_container_base:
if: false # Temporarily disable workflow
runs-on: ubuntu-20.04
runs-on: ubuntu-22.04
steps:
- name: Checkout
uses: actions/checkout@v2
uses: actions/checkout@v4
- name: Set image tag
id: image_tag
run: |
if [ "${GITHUB_REF#refs/heads/}" = "master" ]; then
echo "::set-output name=image_tag::latest";
echo "image_tag=latest" >> $GITHUB_OUTPUT;
else
echo "::set-output name=image_tag::${GITHUB_REF#refs/heads/}"
echo "image_tag=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT;
fi
- name: Docker Login
run: echo "${{ secrets.docker_registry_password }}" | docker login -u ${{ secrets.docker_registry_username }} --password-stdin ${{ secrets.docker_registry }}
- name: Set up Docker Buildx
id: buildx
uses: crazy-max/ghaction-docker-buildx@v1
uses: docker/setup-buildx-action@v3
with:
buildx-version: v0.3.1
version: v0.17.1
- name: Run Buildx
env:
image_name: galaxy-container-base
Expand All @@ -42,22 +42,22 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v2
uses: actions/checkout@v4
- name: Set image tag
id: image_tag
run: |
if [ "${GITHUB_REF#refs/heads/}" = "master" ]; then
echo "::set-output name=image_tag::latest";
echo "image_tag=latest" >> $GITHUB_OUTPUT;
else
echo "::set-output name=image_tag::${GITHUB_REF#refs/heads/}"
echo "image_tag=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT;
fi
- name: Docker Login
run: echo "${{ secrets.docker_registry_password }}" | docker login -u ${{ secrets.docker_registry_username }} --password-stdin ${{ secrets.docker_registry }}
- name: Set up Docker Buildx
id: buildx
uses: crazy-max/ghaction-docker-buildx@v1
uses: docker/setup-buildx-action@v3
with:
buildx-version: v0.3.1
version: v0.17.1
- name: Run Buildx
env:
image_name: galaxy-cluster-base
Expand Down Expand Up @@ -96,22 +96,22 @@ jobs:
fail-fast: false
steps:
- name: Checkout
uses: actions/checkout@v2
uses: actions/checkout@v4
- name: Set image tag
id: image_tag
run: |
if [ "${GITHUB_REF#refs/heads/}" = "master" ]; then
echo "::set-output name=image_tag::latest";
echo "image_tag=latest" >> $GITHUB_OUTPUT;
else
echo "::set-output name=image_tag::${GITHUB_REF#refs/heads/}"
echo "image_tag=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT;
fi
- name: Docker Login
run: echo "${{ secrets.docker_registry_password }}" | docker login -u ${{ secrets.docker_registry_username }} --password-stdin ${{ secrets.docker_registry }}
- name: Set up Docker Buildx
id: buildx
uses: crazy-max/ghaction-docker-buildx@v1
uses: docker/setup-buildx-action@v3
with:
buildx-version: v0.3.1
version: v0.17.1
- name: Run Buildx
run: |
for i in {1..4}; do
Expand All @@ -134,69 +134,43 @@ jobs:
infrastructure:
- name: galaxy-base
files: -f docker-compose.yml
exclude_test:
- workflow_example1
- name: galaxy-proxy-prefix
files: -f docker-compose.yml
env: GALAXY_PROXY_PREFIX=/arbitrary_Galaxy-prefix GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL=http://localhost/arbitrary_Galaxy-prefix
env: GALAXY_PROXY_PREFIX=/arbitrary_Galaxy-prefix GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL=http://localhost/arbitrary_Galaxy-prefix EXTRA_SKIP_TESTS_BIOBLEND="not test_import_export_workflow_dict and not test_import_export_workflow_from_local_path"
exclude_test:
- workflow_example1
- selenium
- name: galaxy-htcondor
files: -f docker-compose.yml -f docker-compose.htcondor.yml
exclude_test:
- workflow_example1
- name: galaxy-slurm
files: -f docker-compose.yml -f docker-compose.slurm.yml
env: SLURM_NODE_COUNT=3
options: --scale slurm_node=3
exclude_test:
- workflow_example1
- name: galaxy-pulsar
files: -f docker-compose.yml -f docker-compose.pulsar.yml
exclude_test:
- workflow_example1
- workflow_mapping_by_sequencing
# - name: galaxy-pulsar-mq
# files: -f docker-compose.yml -f docker-compose.pulsar.yml -f docker-compose.pulsar.mq.yml
# exclude_test:
# - workflow_example1
# - workflow_mapping_by_sequencing
- workflow_quality_control
env: EXTRA_SKIP_TESTS_BIOBLEND="not test_wait_for_job"
- name: galaxy-pulsar-mq
files: -f docker-compose.yml -f docker-compose.pulsar.yml -f docker-compose.pulsar.mq.yml
exclude_test:
- workflow_quality_control
env: EXTRA_SKIP_TESTS_BIOBLEND="not test_wait_for_job"
- name: galaxy-k8s
files: -f docker-compose.yml -f docker-compose.k8s.yml
exclude_test:
- bioblend
- workflow_example1
- workflow_ard
- workflow_mapping_by_sequencing
- selenium
- name: galaxy-singularity
files: -f docker-compose.yml -f docker-compose.singularity.yml
env: EXTRA_SKIP_TESTS_BIOBLEND="not test_get_container_resolvers and not test_show_container_resolver"
- name: galaxy-pulsar-mq-singularity
files: -f docker-compose.yml -f docker-compose.pulsar.yml -f docker-compose.pulsar.mq.yml -f docker-compose.singularity.yml
env: EXTRA_SKIP_TESTS_BIOBLEND="not test_wait_for_job and not test_get_container_resolvers and not test_show_container_resolver"
exclude_test:
- bioblend
- workflow_ard
- workflow_mapping_by_sequencing
- selenium
# - name: galaxy-pulsar-mq-singularity
# files: -f docker-compose.yml -f docker-compose.pulsar.yml -f docker-compose.pulsar.mq.yml -f docker-compose.singularity.yml
# exclude_test:
# - bioblend
# - workflow_ard
# - workflow_mapping_by_sequencing
# - selenium
- workflow_quality_control
- name: galaxy-slurm-singularity
files: -f docker-compose.yml -f docker-compose.slurm.yml -f docker-compose.singularity.yml
exclude_test:
- bioblend
- workflow_ard
- workflow_mapping_by_sequencing
- selenium
env: EXTRA_SKIP_TESTS_BIOBLEND="not test_get_container_resolvers and not test_show_container_resolver"
- name: galaxy-htcondor-singularity
files: -f docker-compose.yml -f docker-compose.htcondor.yml -f docker-compose.singularity.yml
exclude_test:
- bioblend
- workflow_ard
- workflow_mapping_by_sequencing
- selenium
env: EXTRA_SKIP_TESTS_BIOBLEND="not test_get_container_resolvers and not test_show_container_resolver"
test:
- name: bioblend
files: -f tests/docker-compose.test.yml -f tests/docker-compose.test.bioblend.yml
Expand All @@ -209,10 +183,10 @@ jobs:
workflow: sklearn/ard/ard.ga
timeout: 60
second_run: "true"
- name: workflow_mapping_by_sequencing
- name: workflow_quality_control
files: -f tests/docker-compose.test.yml -f tests/docker-compose.test.workflows.yml
exit-from: galaxy-workflow-test
workflow: training/variant-analysis/mapping-by-sequencing/mapping_by_sequencing.ga
workflow: training/sequence-analysis/quality-control/quality_control.ga
timeout: 60
- name: workflow_example1
files: -f tests/docker-compose.test.yml -f tests/docker-compose.test.workflows.yml
Expand All @@ -230,9 +204,9 @@ jobs:
- name: Check if test should be run
id: run_check
if: contains(matrix.infrastructure.exclude_test, matrix.test.name) != true
run: echo ::set-output name=run::true
run: echo "run=true" >> $GITHUB_OUTPUT
- name: Checkout
uses: actions/checkout@v2
uses: actions/checkout@v4
- name: Set image tag in env
run: echo "IMAGE_TAG=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
- name: Master branch - Set image to to 'latest'
Expand All @@ -241,6 +215,9 @@ jobs:
- name: Set WORKFLOWS env for worfklows-test
if: matrix.test.workflow
run: echo "WORKFLOWS=${{ matrix.test.workflow }}" >> $GITHUB_ENV
- name: Install Docker Compose
run: |
sudo apt-get update -qq && sudo apt-get install docker-compose -y
- name: Run tests for the first time
if: steps.run_check.outputs.run
run: |
Expand Down Expand Up @@ -271,11 +248,15 @@ jobs:
shell: bash
working-directory: ./compose
continue-on-error: false
- name: Fix file names before saving artifacts
if: failure()
run: |
sudo find ./compose/export/galaxy/database -depth -name '*:*' -execdir bash -c 'mv "$1" "${1//:/-}"' bash {} \;
- name: Allow upload-artifact read access
if: failure()
run: sudo chmod -R +r ./compose/export/galaxy/database
- name: Save artifacts for debugging a failed test
uses: actions/upload-artifact@v1
uses: actions/upload-artifact@v4
if: failure()
with:
name: ${{ matrix.infrastructure.name }}_${{ matrix.test.name }}_first-run
Expand All @@ -287,7 +268,7 @@ jobs:
sudo rm -rf export/galaxy/database
working-directory: ./compose
- name: Run tests a second time
if: matrix.test.second_run == 'true' && steps.run_check.run
if: matrix.test.second_run == 'true' && steps.run_check.outputs.run
run: |
export DOCKER_REGISTRY=${{ secrets.docker_registry }}
export DOCKER_REGISTRY_USERNAME=${{ secrets.docker_registry_username }}
Expand All @@ -313,11 +294,15 @@ jobs:
shell: bash
working-directory: ./compose
continue-on-error: false
- name: Fix file names before saving artifacts
if: failure() && matrix.test.second_run == 'true'
run: |
sudo find ./compose/export/galaxy/database -depth -name '*:*' -execdir bash -c 'mv "$1" "${1//:/-}"' bash {} \;
- name: Allow upload-artifact read access
if: failure() && matrix.test.second_run == 'true'
run: sudo chmod -R +r ./compose/export/galaxy/database
- name: Save artifacts for debugging a failed test
uses: actions/upload-artifact@v1
uses: actions/upload-artifact@v4
if: failure() && matrix.test.second_run == 'true'
with:
name: ${{ matrix.infrastructure.name }}_${{ matrix.test.name }}_second-run
Expand Down
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