exposed cdhit length requirement in gene family clustering steps to a… #168

	name: panaroo-CI

	on:
	push:
	branches:
	- master
	- devel
	pull_request:
	branches:
	- master
	- devel
	schedule:
	- cron: '1 1 1 * *'


	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.7, 3.8, 3.9]
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install cd-hit
	sudo apt-get install mafft
	wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
	tar -xvf mash-Linux64-v2.2.tar
	sudo cp ./mash-Linux64-v2.2/mash /usr/bin/mash
	python --version
	pip install -U pip
	pip install -U pytest
	wget https://github.com/gtonkinhill/panaroo_test_data/releases/download/v0.0.2/travis_test_data.zip
	unzip travis_test_data.zip

	- name: Install
	run: pip install .

	- name: Validation Tests
	run: pytest -W ignore -q --datafolder="${{ github.workspace }}/travis_test_data/"

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