Add files via upload #15
Workflow file for this run
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# This workflow will install Python dependencies, run tests and lint with a single version of Python | |
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
name: Python application | |
on: | |
push: | |
branches: [ "refactoring" ] | |
permissions: | |
contents: read | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python 3.10 | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.10" | |
- name: Conda installation | |
run: | | |
mkdir -p ~/miniconda3 | |
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh | |
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 | |
rm -rf ~/miniconda3/miniconda.sh | |
~/miniconda3/bin/conda init bash | |
~/miniconda3/bin/conda init zsh | |
- name: Strainy Install | |
run: | | |
#cd strainy | |
ls | |
git submodule update --init | |
make -C submodules/Flye | |
conda env create -f environment.yml -n strainy | |
- name: Test strainy | |
run: | | |
conda run -n strainy ./strainy.py --gfa test_set/toy.gfa --fastq test_set/toy.fastq.gz --output out_strainy --mode hifi --threads 16 | |
- name: Check gfa | |
run: | | |
pip install -U pytest | |
pip install gfapy | |
pytest test_set/toy.py | |