Updated README.md #57
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name: ci | |
on: | |
push: | |
branches: | |
- master | |
- main | |
- final-cleanup | |
- rename-repo-astral | |
permissions: | |
contents: write | |
jobs: | |
deploy: | |
name: Deploy Job | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout Code | |
uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.x | |
- name: Cache dependencies | |
uses: actions/cache@v2 | |
with: | |
key: ${{ github.ref }} | |
path: .cache | |
- name: Download and Unzip Genomes | |
run: | | |
mkdir -p test/test_data | |
while IFS= read -r link; do | |
file_name=$(basename "$link") | |
wget -O "test/test_data/$file_name" "$link" | |
done < test/input_genome_links.txt | |
- name: Set up Conda | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniforge-variant: Mambaforge | |
channels: conda-forge, bioconda | |
activate-environment: roadies_env_test | |
environment-file: test/roadies_env_test.yaml | |
- name: Run Tests | |
shell: bash -l {0} | |
run: | | |
chmod +x test/roadies_env_test.sh | |
source test/roadies_env_test.sh | |
pip3 install ete3 six numpy PyYAML | |
python run_roadies.py --cores 32 --config test/test_config.yaml --mode accurate | |
- name: Install dependencies for mkdocs | |
run: | | |
pip install mkdocs-material | |
pip install "mkdocs-material[imaging]" | |
- run: mkdocs gh-deploy --force |