Merge pull request #390 from ASLeonard/optionally_missing_tools #885

	on: [push]

	name: build and test docker image

	jobs:
	build_and_test:
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	- name: Build the Docker image
	run: docker build . --file Dockerfile --target binary --tag pggb
	- name: Run a test on the DRB1-3123 dataset (SPOA)
	run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 800,900,1100 -n 10 -t 2 -Z -M -m -o drib1_spoa && ls drib1_spoa/* && head drib1_spoa/*.log -n 63"
	- name: Run a test on the DRB1-3123 dataset (abPOA)
	run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 800,900,1100 -n 10 -t 2 -Z -M -m -b -o drib1_abpoa && ls drib1_abpoa/* && head drib1_abpoa/*.log -n 63"
	- name: Run a test on the DRB1-3123 dataset (paf)
	run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -a data/paf/DRB1-3123.fa.15a1009.wfmash.paf -p 70 -s 3000 -G 2000 -n 10 -t 2 -Z -M -m -o drib1_paf && ls drib1_paf/* && head drib1_paf/*.log -n 63"
	- name: Run a test on the LPA dataset (SPOA global)
	run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/LPA/LPA.fa.gz -p 95 -s 20000 -G 800,900 -k 79 -t 2 -Z -O 0.001 -m -z -o lpa -V 'chm13,chm1:1000' && ls lpa/* && head lpa/*.log -n 63"
	- name: Run a test for the gfa2evaluation script on a mini HPRC chrMT dataset
	run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "gfa2evaluation.sh data/chrM.pan.4.gfa chm13 data/test_eval 2"

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