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build.yaml
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name: Mykrobe builds
on:
push:
tags:
- 'v*.*.*'
branches:
- master
pull_request:
branches:
- master
env:
REGISTRY: ghcr.io
IMAGE_NAME: ${{ github.repository }}
jobs:
build_containers:
name: Build linux/singularity container
runs-on: ubuntu-20.04
steps:
- name: Set up Go 1.16
uses: actions/setup-go@v1
with:
go-version: 1.16
id: go
- name: Install Dependencies
run: |
sudo apt-get update && sudo apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
pkg-config \
debootstrap \
debian-keyring \
debian-archive-keyring \
rsync
- name: Install Singularity
env:
SINGULARITY_VERSION: 3.5.3
GOPATH: /tmp/go
run: |
mkdir -p $GOPATH
sudo mkdir -p /usr/local/var/singularity/mnt
mkdir -p $GOPATH/src/github.com/sylabs
cd $GOPATH/src/github.com/sylabs
wget https://github.com/hpcng/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz
tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz
cd singularity
./mconfig -v -p /usr/local
make -j `nproc 2>/dev/null || echo 1` -C ./builddir all
sudo make -C ./builddir install
- name: Check out code for the container build
uses: actions/checkout@v3
- name: Set release version if is a release
if: startsWith(github.event.ref, 'refs/tags/v')
run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
- name: Set release version if not a release
if: false == startsWith(github.event.ref, 'refs/tags/v')
run: echo "RELEASE_VERSION=test" >> $GITHUB_ENV
- name: Build Singularity container
env:
SINGULARITY_RECIPE: Singularity.def
OUTPUT_CONTAINER: mykrobe_${{env.RELEASE_VERSION}}.img
run: |
ls
if [ -f "${SINGULARITY_RECIPE}" ]; then
sudo -E singularity build ${OUTPUT_CONTAINER} ${SINGULARITY_RECIPE}
else
echo "${SINGULARITY_RECIPE} is not found."
echo "Present working directory: $PWD"
ls
fi
- name: Release
if: startsWith(github.event.ref, 'refs/tags/v')
uses: softprops/action-gh-release@v1
with:
files: mykrobe*.img
draft: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
mac_build:
name: Build mac os command line
runs-on: macos-11
steps:
- name: Check out code for the build
uses: actions/checkout@v3
- uses: actions/setup-python@v4
with:
python-version: '3.8'
- name: Install dependencies
run: |
git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex mccortex
cd mccortex
make MAXK=31
cd ..
cp mccortex/bin/mccortex31 src/mykrobe/cortex/
python -m pip install -r requirements.txt wheel pyinstaller
sudo python -m pip install .
- name: Set release version if is a release
if: startsWith(github.event.ref, 'refs/tags/v')
run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
- name: Set release version if not a release
if: false == startsWith(github.event.ref, 'refs/tags/v')
run: echo "RELEASE_VERSION=test" >> $GITHUB_ENV
- name: Test and build command line tarball
env:
OUTPUT_TARBALL: mykrobe.command_line.osx.${{env.RELEASE_VERSION}}.tar.gz
run: |
# mongod default data directory is /data/db, which is not writeable.
mkdir $HOME/mongodb_data
chown -R `id -un` $HOME/mongodb_data
sudo mongod --dbpath=$HOME/mongodb_data --quiet &> /dev/null &
sleep 3s
pytest --cov-report term-missing --cov=mykrobe
mykrobe panels update_metadata --panels_dir src/mykrobe/data
mykrobe panels update_species --panels_dir src/mykrobe/data --debug all
cd dist
pyinstaller --workpath='./pyinstaller_build/binary_cache' --distpath='./pyinstaller_build' mykrobe_atlas_pyinstaller.spec
cd pyinstaller_build
tar cvfz ../../${OUTPUT_TARBALL} mykrobe_atlas/
- name: Release
if: startsWith(github.event.ref, 'refs/tags/v')
uses: softprops/action-gh-release@v1
with:
files: mykrobe.command_line.osx.*.tar.gz
draft: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
windows_build:
name: Build Windows command line
runs-on: windows-2019
steps:
- uses: msys2/setup-msys2@v2
with:
update: true
install: >-
autotools gcc git libcurl-devel bzip2 liblzma zip libbz2-devel xz zlib zlib-devel libtool wget liblzma-devel ncurses-devel base-devel openssl-devel mingw64/mingw-w64-x86_64-python3 mingw64/mingw-w64-x86_64-python3-pip mingw-w64-x86_64-python3-numpy mingw-w64-x86_64-python3-setuptools mingw-w64-x86_64-python3-wheel mingw-w64-x86_64-python-biopython
- name: Check out code for the build
uses: actions/checkout@v3
- name: Set release version if is a release
if: startsWith(github.event.ref, 'refs/tags/v')
run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
shell: msys2 {0}
- name: Set release version if not a release
if: false == startsWith(github.event.ref, 'refs/tags/v')
run: echo "RELEASE_VERSION=test" >> $GITHUB_ENV
shell: msys2 {0}
- name: Start MongoDB service
run: |
sc.exe config MongoDB start= auto
sc.exe start MongoDB
- name: Test and build command line tarball
env:
OUTPUT_TARBALL: mykrobe.command_line.windows.${{env.RELEASE_VERSION}}.tar.gz
run: |
export PYTHONPATH="/mingw64/lib/python3.11/:/mingw64/lib/python3.11/site-packages:${PYTHONPATH}"
C:\\msys64\\mingw64\\bin\\python3.exe -m ensurepip --upgrade
C:\\msys64\\mingw64\\bin\\python3.exe -m pip install pyinstaller requests pytest
echo "clone mccortex"
rm -rf mccortex
git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex
cd mccortex/libs/htslib
git checkout bcf9bff178f81c9c1cf3a052aeb6cbe32fe5fdcc
cd ../bcftools
git checkout b406a3906b153faa8bec0a53df07b2adf18a3052
cd ../samtools
git checkout 2d4907cf9a34ccf7cde60143158b39e1cb40ac0c
cd ../../../
python ./ci/windows_file_fixes.py
cd mccortex
echo "make mccortex"
make all
echo "make tests mccortex"
make tests
cd ..
echo "pip install requirements"
C:\\msys64\\mingw64\\bin\\python3.exe -m pip install -r requirements.txt
echo "pip install ."
C:\\msys64\\mingw64\\bin\\python3.exe -m pip install .
echo "pytest"
export MYKROBE_MCCORTEX="${PWD}/mccortex/bin/mccortex31"
C:\\msys64\\mingw64\\bin\\python3.exe -m pytest
echo "update panels"
C:\\msys64/mingw64/bin/mykrobe.exe panels update_metadata --panels_dir src/mykrobe/data
C:\\msys64/mingw64/bin/mykrobe.exe panels update_species --panels_dir src/mykrobe/data --debug all
cd dist
C:\\msys64/mingw64/bin/pyinstaller.exe --workpath='./pyinstaller_build/binary_cache' --distpath='./pyinstaller_build' mykrobe_atlas_pyinstaller_windows.spec
cd pyinstaller_build
tar cvfz ../../${OUTPUT_TARBALL} mykrobe_atlas/
shell: msys2 {0}
- name: Release
if: startsWith(github.event.ref, 'refs/tags/v')
uses: softprops/action-gh-release@v1
with:
files: mykrobe.command_line.windows.*.tar.gz
draft: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}