Apptainer Run #36

	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_denovo --input-directory test/data/ --use-apptainer && cd denovo && sh denovo.sh

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