Apptainer Run #72
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name: Apptainer Run | |
on: | |
push: | |
branches: | |
- main | |
- dev | |
workflow_dispatch: | |
pull_request: | |
branches-ignore: [] | |
schedule: | |
- cron: '0 0 20 * *' | |
jobs: | |
build-linux: | |
runs-on: ubuntu-latest | |
strategy: | |
max-parallel: 5 | |
matrix: | |
python: [3.8, '3.10'] | |
fail-fast: false | |
steps: | |
- name: precleanup | |
run: | | |
sudo rm -rf /usr/share/dotnet | |
sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
- name: install graphviz | |
run: | | |
sudo apt update | |
sudo apt-get install -y graphviz software-properties-common | |
sudo add-apt-repository -y ppa:apptainer/ppa | |
sudo apt update | |
sudo apt install -y apptainer | |
- name: checkout git repo | |
uses: actions/checkout@v3 | |
- name: Set up Python 3.X | |
uses: actions/setup-python@v3 | |
with: | |
python-version: ${{ matrix.python }} | |
- name: Install dependencies | |
run: | | |
pip install .[testing] | |
- name: install package itself | |
run: | | |
pip install . | |
pip install "pulp==2.7.0" --no-deps | |
- name: testing | |
run: | | |
sequana_rnaseq --aligner-choice bowtie2 --input-directory test/data/ --use-apptainer --genome-directory test/data/Saccer3 && cd rnaseq && sh rnaseq.sh | |