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merged unitig bam

merged unitig bam #16

Workflow file for this run

# 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