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azure-pipelines.yml
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azure-pipelines.yml
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jobs:
- job: mac_latest_gcc
pool:
vmImage: macOS-latest
steps:
- script: |
find /usr/local/bin -lname '*/Library/Frameworks/Python.framework/*' -delete # Trying solution from https://github.com/mesonbuild/meson/blob/master/.github/workflows/macos.yml#L87-L92
sudo rm -rf /Library/Frameworks/Python.framework/
brew install --force python3 node@18 && brew unlink python3 node@18 && brew unlink python3 node@18 && brew link --overwrite python3 node@18
find /usr/local/Cellar/python* -name EXTERNALLY-MANAGED -print0 | xargs -0 rm -vf
brew update
brew install automake boost openmpi google-sparsehash make pandoc ghc gcc@14 llvm
displayName: Install common
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.5.0/btllib-1.5.0.tar.gz
export CC=gcc-14
export CXX=g++-14
tar xzf btllib-1.5.0.tar.gz
cd btllib-1.5.0
./compile
displayName: Install btllib
- script: |
./autogen.sh
export CC=gcc-14
export CXX=g++-14
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-14 CXX=g++-14 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.0/install"
./configure CC=gcc-14 CXX=g++-14 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.0/install
make -j12 distcheck AM_CXXFLAGS=-Wno-error=dangling-reference
displayName: Compiling ABySS with gcc-14
- job:
displayName: mac_latest-compilers-clang
pool:
vmImage: 'macOS-latest'
steps:
- script: |
mkdir -p ~/miniforge3
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh -o ~/miniforge3/miniforge.sh
bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
rm -rf ~/miniforge3/miniforge.sh
~/miniforge3/bin/conda init bash
~/miniforge3/bin/conda init zsh
export CONDA=$(realpath ~/miniforge3/bin)
echo "##vso[task.prependpath]$CONDA"
displayName: Install conda
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi automake perl pandoc meson ninja btllib
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
displayName: Compiling ABySS
- job:
displayName: mac_clang16
pool:
vmImage: 'macOS-latest'
steps:
- script: |
mkdir -p ~/miniforge3
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh -o ~/miniforge3/miniforge.sh
bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
rm -rf ~/miniforge3/miniforge.sh
~/miniforge3/bin/conda init bash
~/miniforge3/bin/conda init zsh
export CONDA=$(realpath ~/miniforge3/bin)
echo "##vso[task.prependpath]$CONDA"
displayName: Install conda
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
mamba install --yes -c conda-forge -c bioconda compilers=1.7.0 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
displayName: Compiling ABySS with clang 16
- job:
displayName: mac_clang15
pool:
vmImage: 'macOS-latest'
steps:
- script: |
mkdir -p ~/miniforge3
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh -o ~/miniforge3/miniforge.sh
bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
rm -rf ~/miniforge3/miniforge.sh
~/miniforge3/bin/conda init bash
~/miniforge3/bin/conda init zsh
export CONDA=$(realpath ~/miniforge3/bin)
echo "##vso[task.prependpath]$CONDA"
displayName: Install conda
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
mamba install --yes -c conda-forge -c bioconda compilers=1.6.0 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
displayName: Compiling ABySS with clang 15
- job:
displayName: mac_clang14
pool:
vmImage: 'macOS-latest'
steps:
- script: |
mkdir -p ~/miniforge3
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh -o ~/miniforge3/miniforge.sh
bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
rm -rf ~/miniforge3/miniforge.sh
~/miniforge3/bin/conda init bash
~/miniforge3/bin/conda init zsh
export CONDA=$(realpath ~/miniforge3/bin)
echo "##vso[task.prependpath]$CONDA"
displayName: Install conda
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck
displayName: Compiling ABySS with clang 14
- job:
displayName: mac_clang13
pool:
vmImage: 'macOS-latest'
steps:
- script: |
mkdir -p ~/miniforge3
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh -o ~/miniforge3/miniforge.sh
bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
rm -rf ~/miniforge3/miniforge.sh
~/miniforge3/bin/conda init bash
~/miniforge3/bin/conda init zsh
export CONDA=$(realpath ~/miniforge3/bin)
echo "##vso[task.prependpath]$CONDA"
displayName: Install conda
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck
displayName: Compiling ABySS with clang 13
- job: linux_gcc12
pool:
vmImage: ubuntu-latest
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-12 g++-12
displayName: Install gcc-12
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
tar xzf btllib-1.7.2.tar.gz
cd btllib-1.7.2
export CC=gcc-12
export CXX=g++-12
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-12 CXX=g++-12 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
./configure CC=gcc-12 CXX=g++-12 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-12
- job: linux_gcc11
pool:
vmImage: ubuntu-latest
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-11 g++-11
displayName: Install gcc-11
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
tar xzf btllib-1.7.2.tar.gz
cd btllib-1.7.2
export CC=gcc-11
export CXX=g++-11
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-11 CXX=g++-11 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
./configure CC=gcc-11 CXX=g++-11 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-11
- job: linux_gcc10
pool:
vmImage: ubuntu-20.04
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-10 g++-10
displayName: Install gcc-10
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
tar xzf btllib-1.7.2.tar.gz
cd btllib-1.7.2
export CC=gcc-10
export CXX=g++-10
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-10 CXX=g++-10 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
./configure CC=gcc-10 CXX=g++-10 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-10
- script: |
curl https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
sudo apt-add-repository "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main"
sudo apt-get update
sudo apt-get install -y --no-install-recommends clang-format-8
sudo ln -sf clang-format-8 /usr/bin/clang-format
displayName: Install clang-format
- script: make clang-format
displayName: Run clang-format
- job: linux_gcc9
pool:
vmImage: ubuntu-latest
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-9 g++-9
displayName: Install gcc-9
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
tar xzf btllib-1.7.2.tar.gz
cd btllib-1.7.2
export CC=gcc-9
export CXX=g++-9
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-9 CXX=g++-9 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
./configure CC=gcc-9 CXX=g++-9 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-9
- job: linux_gcc8
pool:
vmImage: ubuntu-latest
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu focal main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu focal-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-8 g++-8
displayName: Install gcc-8
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.6.0/btllib-1.6.0.tar.gz
tar xzf btllib-1.6.0.tar.gz
cd btllib-1.6.0
export CC=gcc-8
export CXX=g++-8
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8 --with-btllib=/home/vsts/work/1/s/btllib-1.6.0/install"
./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.6.0/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-8
- job:
displayName: linux_gcc-latest
pool:
vmImage: 'ubuntu-latest'
steps:
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
conda install --yes -c conda-forge mamba python=3.9
mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi util-linux perl btllib pandoc
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck AM_CXXFLAGS=-Wall CXXFLAGS='-pthread'
displayName: Compiling ABySS with gcc