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basic.yml
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name: SPAdes basic tests
on:
workflow_dispatch:
push:
branches:
- master
- main
- next
tags:
- '*'
paths-ignore:
- 'docs/**'
- 'mkdocs.yml'
pull_request:
paths-ignore:
- 'docs/**'
- 'mkdocs.yml'
env:
BUILD_TYPE: Release
BUILD_DIR: './build'
SRC_DIR: './src'
INSTALL_DIR: ${{github.workspace}}/spades
PKG_LINUX: SPAdes-*-Linux
PKG_MAC: SPAdes-*-Darwin
jobs:
build-linux:
runs-on: self-hosted
name: '🐧 Build SPAdes for Linux'
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: '⚙️ Install ccache'
uses: hendrikmuhs/ccache-action@v1.2
with:
variant: sccache
key: sccache-${{env.BUILD_TYPE}}-linux
- name: '⚙️ Configure CMake'
run: >
cmake
-B $BUILD_DIR
-S $SRC_DIR
-DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all
-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
- name: '🚧 Build'
run: >
cmake
--build ${{env.BUILD_DIR}}
-j16
-t package include_test debruijn_test
- name: '📦 Package'
uses: actions/upload-artifact@v4
with:
name: build-artifacts-linux
path: |
${{env.BUILD_DIR}}/${{env.PKG_LINUX}}.tar.gz
${{env.BUILD_DIR}}/bin/debruijn_test
${{env.BUILD_DIR}}/bin/include_test
spades-1k-checks-linux:
name: '🚬 E. coli 1k smoke checks'
runs-on: self-hosted
needs: build-linux
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '📦 Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-linux
path: ${{env.INSTALL_DIR}}
- name: '📦 Unpack package'
working-directory: ${{env.INSTALL_DIR}}
run: >
tar -zxf $PKG_LINUX.tar.gz
- name: '1k multi-cell'
run: >
$INSTALL_DIR/$PKG_LINUX/bin/spades.py --test
- name: '1k single-cell'
run: >
$INSTALL_DIR/$PKG_LINUX/bin/spades.py --sc --test
- name: '1k meta'
run: >
$INSTALL_DIR/$PKG_LINUX/bin/metaspades.py --test
- name: '1k plasmid'
run: >
$INSTALL_DIR/$PKG_LINUX/bin/plasmidspades.py --test
- name: '1k rna'
run: >
$INSTALL_DIR/$PKG_LINUX/bin/rnaspades.py --test
- name: '1k corona'
run: >
$INSTALL_DIR/$PKG_LINUX/bin/coronaspades.py --test
spades-unittests-linux:
name: 'SPAdes unittests'
runs-on: self-hosted
needs: build-linux
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-linux
path: ${{env.BUILD_DIR}}
- name: '🔎 Include tests'
working-directory: ${{github.workspace}}
run: >
chmod +x $BUILD_DIR/bin/include_test &&
$BUILD_DIR/bin/include_test
- name: '🔎 De-Bruijn tests'
working-directory: ${{github.workspace}}
run: >
chmod +x $BUILD_DIR/bin/debruijn_test &&
$BUILD_DIR/bin/debruijn_test
build-mac:
strategy:
matrix:
include:
- os: macos-13
arch: x86_64
- os: macos-14
arch: arm64
name: '🍎 Build SPAdes for macOS'
runs-on: ${{ matrix.os }}
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: '⚙️ Install dependencies'
run: >
brew install llvm libomp bzip2
- name: '⚙️ Install ccache'
uses: hendrikmuhs/ccache-action@v1.2
with:
variant: sccache
key: sccache-${{env.BUILD_TYPE}}-${{ matrix.os }}
- name: '⚙️ Configure CMake'
run: >
cmake
-B $BUILD_DIR
-S $SRC_DIR
-DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all
-DCMAKE_C_COMPILER=$(brew --prefix llvm)/bin/clang
-DCMAKE_CXX_COMPILER=$(brew --prefix llvm)/bin/clang++
-DCMAKE_EXE_LINKER_FLAGS=-L$(brew --prefix llvm)/lib/c++
-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
- name: '🚧 Build'
run: >
cmake
--build $BUILD_DIR
-j16
-t package include_test debruijn_test
- name: '📦 Package'
uses: actions/upload-artifact@v4
with:
name: build-artifacts-mac-${{ matrix.arch }}
path: |
${{env.BUILD_DIR}}/${{env.PKG_MAC}}.tar.gz
${{env.BUILD_DIR}}/bin/debruijn_test
${{env.BUILD_DIR}}/bin/include_test
spades-1k-checks-mac:
name: '🚬 E. coli 1k smoke checks'
strategy:
matrix:
include:
- os: macos-13
arch: x86_64
- os: macos-14
arch: arm64
runs-on: ${{ matrix.os }}
needs: build-mac
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '⚙️ Install dependencies'
run: >
brew install llvm libomp bzip2
- name: '📦 Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-mac-${{ matrix.arch }}
path: ${{env.INSTALL_DIR}}
- name: '📦 Unpack package'
working-directory: ${{env.INSTALL_DIR}}
run: >
tar -zxf ${{env.PKG_MAC}}.tar.gz
- name: '1k multi-cell'
run: >
$INSTALL_DIR/$PKG_MAC/bin/spades.py --test
- name: '1k single-cell'
run: >
$INSTALL_DIR/$PKG_MAC/bin/spades.py --sc --test
- name: '1k meta'
run: >
$INSTALL_DIR/$PKG_MAC/bin/metaspades.py --test
- name: '1k plasmid'
run: >
$INSTALL_DIR/$PKG_MAC/bin/plasmidspades.py --test
- name: '1k rna'
run: >
$INSTALL_DIR/$PKG_MAC/bin/rnaspades.py --test
- name: '1k corona'
run: >
$INSTALL_DIR/$PKG_MAC/bin/coronaspades.py --test
spades-unittests-mac:
name: 'SPAdes unittests'
strategy:
matrix:
include:
- os: macos-13
arch: x86_64
- os: macos-14
arch: arm64
runs-on: ${{ matrix.os }}
needs: build-mac
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-mac-${{ matrix.arch }}
path: ${{env.BUILD_DIR}}
- name: '⚙️ Install dependencies'
run: >
brew install llvm libomp bzip2
- name: '🔎 Include tests'
working-directory: ${{github.workspace}}
run: >
chmod +x $BUILD_DIR/bin/include_test &&
$BUILD_DIR/bin/include_test
- name: '🔎 De-Bruijn tests'
working-directory: ${{github.workspace}}
run: >
chmod +x $BUILD_DIR/bin/debruijn_test &&
$BUILD_DIR/bin/debruijn_test