Build

uploaded workflow charts #183

	name: Build

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

	jobs:
	build-linux-x86-64:
	name: Linux x86-64
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -el {0}

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	activate-environment: eukfinder
	environment-file: eukfinder_env.yml
	auto-activate-base: false

	- name: Verify Conda env
	run: \|
	conda info
	conda list
	conda env list
	conda activate eukfinder

	- name: Install dependencies
	run: \|
	sudo wget https://github.com/PLAST-software/plast-library/releases/download/v2.3.2/plastbinary_linux_v2.3.2.tar.gz
	sudo apt-get update
	sudo apt-get install -y tar

	- name: Setup PLAST binaries
	run: \|
	tar -zxf plastbinary_linux_v2.3.2.tar.gz

	- name: Verify PLAST installation
	run: \|
	export PATH=$PWD/plastbinary_linux_v2.3.2/build/bin:$PATH
	plast -h \|\| { echo 'PLAST installation failed'; exit 1; }

	- name: Clone acc2tax repository
	run: \|
	git clone https://github.com/richardmleggett/acc2tax.git

	- name: Build acc2tax
	run: \|
	cd acc2tax
	gcc -o acc2tax acc2tax.c

	- name: Verify acc2tax build
	run: \|
	cd acc2tax
	./acc2tax --help \|\| { echo 'acc2tax build failed'; exit 1; }

	- name: Generate executable
	run: \|
	python setup.py install --single-version-externally-managed --record=record.txt

	- name: Verify eukfinder sub-calls
	run: \|
	eukfinder read_prep -h
	eukfinder short_seqs -h
	eukfinder long_seqs -h

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