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ensembl-production.yml
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name: Ensembl/ensembl-production
env:
MYSQL_ROOT_PASSWORD: ensembl
on:
push:
branches:
- "**/*"
pull_request:
schedule:
- cron: "0 0 * * 1"
jobs:
test:
runs-on: ubuntu-latest
steps:
- name: checkout
uses: actions/[email protected]
- uses: shogo82148/[email protected]
with:
perl-version: "${{ matrix.perl }}"
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
- run: export PATH=$PATH:$PWD/ensembl-git-tools/bin
- run: export ENSEMBL_BRANCH=master
- run: export SECONDARY_BRANCH=main
- run: echo "TRAVIS_BRANCH=${{ github.ref }}"
- run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi
- run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
- run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
- run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
- run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
- run: cd htslib
- run: make
- run: export HTSLIB_DIR=$(pwd -P)
- run: cd ..
- run: cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
- run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
- run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
- run: export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
- run: cpanm --sudo -v --installdeps --notest .
- run: cpanm --sudo -n Devel::Cover::Report::Coveralls
- run: cp travisci/MultiTestDB.conf.travisci modules/t/MultiTestDB.conf
- run: mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
- run: "./travisci/harness.sh"
- uses: rtCamp/[email protected]
env:
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}"
strategy:
matrix:
perl:
- '5.14'
- 5.26.2
include:
- COVERALLS: 'true'
DB: mysql
services:
mysql:
image: mysql
env:
COVERALLS: "${{ matrix.COVERALLS }}"
DB: "${{ matrix.DB }}"
test_2:
runs-on: ubuntu-latest
env:
COVERALLS: 'true'
DB: mysql
steps:
- name: checkout
uses: actions/[email protected]
- uses: actions/[email protected]
with:
python-version: 3.7.6
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
- run: export PATH=$PATH:$PWD/ensembl-git-tools/bin
- run: export ENSEMBL_BRANCH=master
- run: export SECONDARY_BRANCH=main
- run: echo "TRAVIS_BRANCH=${{ github.ref }}"
- run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi
- run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
- run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
- run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
- run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
- run: cd htslib
- run: make
- run: export HTSLIB_DIR=$(pwd -P)
- run: cd ..
- run: pip install -r requirements-test.txt
- run: pip install -e .
- run: pytest src/python/test
- uses: rtCamp/[email protected]
env:
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}"
services:
mysql:
image: mysql
test_3:
runs-on: ubuntu-latest
env:
COVERALLS: 'true'
DB: mysql
steps:
- name: checkout
uses: actions/[email protected]
- uses: actions/[email protected]
with:
python-version: 3.8
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
- run: export PATH=$PATH:$PWD/ensembl-git-tools/bin
- run: export ENSEMBL_BRANCH=master
- run: export SECONDARY_BRANCH=main
- run: echo "TRAVIS_BRANCH=${{ github.ref }}"
- run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi
- run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
- run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
- run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
- run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
- run: cd htslib
- run: make
- run: export HTSLIB_DIR=$(pwd -P)
- run: cd ..
- run: pip install -r requirements-test.txt
- run: pip install -e .
- run: pytest src/python/test
- uses: rtCamp/[email protected]
env:
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}"
services:
mysql:
image: mysql