Update MQProteogenomics.md #141

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	# trigger workflow

	name: Python application

	on:
	push:
	branches: [ master ]
	pull_request:
	branches: [ master ]

	jobs:
	build:
	runs-on: ubuntu-latest
	container: thyscbio/bio:v3.0.19
	steps:
	- uses: actions/checkout@v2
	#- name: Set up Python 3.8
	# uses: actions/setup-python@v2
	# with:
	# python-version: 3.8
	- name: Install dependencies
	run: \|
	git clone https://[email protected]/thys_potgieter/cbio-proteogenomics-tests.git
	pip3 install --upgrade pip
	pip3 install flake8 pytest
	#if [ -f requirements.txt ]; then pip3 install -r requirements.txt; fi
	- name: Lint with flake8
	run: \|
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: \|
	pwd
	export PATH=$PATH::/__w/proteomics-pipelines/proteomics-pipelines/bin/python:/__w/proteomics-pipelines/proteomics-pipelines/bin/bash:/__w/proteomics-pipelines/proteomics-pipelines/bin/R:/__w/proteomics-pipelines/proteomics-pipelines/bin/perl
	export PYTHONPATH=$PYTHONPATH::/__w/proteomics-pipelines/proteomics-pipelines/lib
	echo $PATH
	cd cbio-proteogenomics-tests/lib && pytest -v

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