New guix build targets and shells. Fixes libasan and adds profiling. #1190

	on:
	push:
	branches: [ main ]
	paths-ignore:
	- '*/.md'
	pull_request:
	branches: [ main ]
	paths-ignore:
	- '*/.md'

	name: build and test

	jobs:
	build_and_test:
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	- name: Install required packages
	run: sudo apt-get update && sudo apt-get install -y
	git
	bash
	cmake
	make
	g++
	python3-dev
	libatomic-ops-dev
	autoconf
	libgsl-dev
	zlib1g-dev
	libdeflate-dev
	libhts-dev
	samtools
	libjemalloc-dev
	bedtools
	- name: Init and update submodules
	run: git submodule update --init --recursive
	- name: Build wfmash
	run: cmake -H. -Bbuild -D CMAKE_BUILD_TYPE=Debug -DWFA_PNG_AND_TSV=ON && cmake --build build -- -j 2
	- name: Run cmake tests
	run: \|
	cd build
	ctest --verbose
	- name: Install Rust and Cargo
	uses: actions-rs/toolchain@v1
	with:
	toolchain: stable
	override: true
	- name: Install wgatools
	run: cargo install --git https://github.com/wjwei-handsome/wgatools.git
	- name: Install wgatools
	run: cargo install --git https://github.com/ekg/pafcheck.git
	- name: Run wfmash and generate PAF
	run: build/bin/wfmash -t 8 -T SGDref -Q S288C -Y '#' data/scerevisiae8.fa.gz > test.paf
	- name: check PAF coordinates and extended CIGAR validity
	run: pafcheck --query-fasta data/scerevisiae8.fa.gz --paf test.paf
	- name: Convert PAF to MAF using wgatools
	run: wgatools paf2maf --target data/scerevisiae8.fa.gz --query data/scerevisiae8.fa.gz test.paf > test.maf
	- name: Check if MAF file is not empty
	run: \|
	if [ -s test.maf ]; then
	echo "MAF file is not empty. Test passed."
	else
	echo "MAF file is empty. Test failed."
	exit 1
	fi

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