index reference genome and create result md5sum #12

	name: CI

	on:
	push:
	branches:
	- '**'
	pull_request:
	branches:
	- main
	- master

	jobs:
	build:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python_version: [2.7, 3.8]
	config:
	- { r: 'release', ggplot: '3.3.3' }
	- { r: 'oldrel', ggplot: '3.3.3' }
	- { r: '3.5.3', ggplot: '2.2.1' }
	steps:
	- uses: actions/checkout@v2
	- name: Setup R
	uses: r-lib/actions/setup-r@v1
	with:
	r-version: ${{ matrix.config.r }}
	- name: Cache R packages
	uses: actions/cache@v2
	with:
	path: ${{ env.R_LIBS_USER }}
	key: ${{ runner.os }}-${{ matrix.config.r }}
	restore-keys: ${{ runner.os }}-${{ matrix.config.r }}
	- name: Install remotes
	run: \|
	install.packages("remotes")
	shell: Rscript {0}
	- name: Install R packages
	run: \|
	remotes::install_version("ggplot2", version="${{ matrix.config.ggplot }}")
	remotes::install_cran(c("gridExtra", "data.table", "svglite"))
	shell: Rscript {0}
	- name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python_version }}
	- name: Cache Python packages
	uses: actions/cache@v2
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade --upgrade-strategy eager pip wheel
	if [ -f requirements.txt ]; then pip install --upgrade --upgrade-strategy eager -r requirements.txt; fi
	if [ -f requirements.dev.txt ]; then pip install --upgrade --upgrade-strategy eager -r requirements.dev.txt; fi
	- name: Test with pytest
	run:
	pytest
	- name: Run CI test script
	run:
	bash .github/workflows/ci.sh

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