11222024 pairedend and readspecific #124

	name: integration_test_cli

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main

	jobs:
	build:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repo content
	uses: actions/checkout@v2

	- name: Install Mamba
	run: \|
	conda install -c conda-forge mamba -y

	- name: Print conda folder contents
	run: \|

	ls /usr/share/miniconda/bin/
	ls /usr/share/miniconda/

	- name: Create Conda Environment
	run: \|
	/usr/share/miniconda/bin/mamba create -n marine_environment python=3.8.18 -y
	/usr/share/miniconda/bin/mamba env update -n marine_environment --file marine_environment2.yaml

	- name: Print marine_environment bin folder contents
	run: \|
	ls /usr/share/miniconda/envs/marine_environment/bin


	- name: Execute Integration Tests
	run: \|
	echo "running source"
	source /home/runner/.bashrc
	echo "running init"
	conda init bash

	CONDA_BASE=$(conda info --base) ; source $CONDA_BASE/etc/profile.d/conda.sh

	echo "running activate"
	conda activate marine_environment

	which python

	echo "creating marine base dir environment variable..."
	export MARINE=$(pwd)
	echo $MARINE
	ls $MARINE

	echo "Adding marine to path..."
	export PATH=$PATH:$(pwd)
	echo $PATH

	echo "running test"
	cd tests
	pwd

	bash integration_tests_run.sh /usr/share/miniconda/envs/marine_environment/bin/python

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