update slow5lib to 1.2-beta #187
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| name: Linux x86_64 | |
| on: | |
| push: | |
| branches: '**' | |
| pull_request: | |
| branches: '**' | |
| jobs: | |
| ubuntu_14_local_hts: | |
| name: ubuntu 14 local hts | |
| runs-on: ubuntu-20.04 | |
| container: ubuntu:14.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: install packages | |
| run: sudo apt-get update && sudo apt-get install -y zlib1g-dev libhdf5-dev gcc g++ autoconf automake make wget | |
| - name: env | |
| run: lsb_release -a && ldd --version && gcc --version && g++ --version | |
| - name: build | |
| run: autoreconf && ./scripts/install-hts.sh && ./configure && make -j8 | |
| - name: test | |
| run: make test | |
| ubuntu_16_install_scripts: | |
| name: Ubuntu 16 install scripts | |
| runs-on: ubuntu-20.04 | |
| container: ubuntu:16.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: install packages | |
| run: apt-get update && apt-get install -y zlib1g-dev valgrind gcc g++ autoconf automake make wget bzip2 | |
| - name: build | |
| run: autoreconf && ./scripts/install-hdf5.sh &&./scripts/install-hts.sh && ./configure --enable-localhdf5 && make -j8 | |
| - name: test | |
| run: make test | |
| - name: test valgrind | |
| run: valgrind --leak-check=full --error-exitcode=1 ./f5c call-methylation -b test/ecoli_2kb_region/reads.sorted.bam -g test/ecoli_2kb_region/draft.fa -r test/ecoli_2kb_region/reads.fasta -t 8 -K 256 -B 2M > /dev/null | |
| ubuntu_16_pure_make: | |
| name: Ubuntu 16 pure make | |
| runs-on: ubuntu-20.04 | |
| container: ubuntu:16.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: install packages | |
| run: apt-get update && apt-get install -y zlib1g-dev gcc g++ autoconf automake make wget bzip2 | |
| - name: build | |
| run: make | |
| - name: test | |
| run: make test | |
| ubuntu_18: | |
| name: Ubuntu 18 | |
| runs-on: ubuntu-20.04 | |
| container: ubuntu:18.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: install packages | |
| run: apt-get update && apt-get install -y zlib1g-dev libhdf5-dev gcc g++ autoconf automake make wget bzip2 | |
| - name: build | |
| run: autoreconf && ./scripts/install-hts.sh && ./configure && make -j8 | |
| - name: test | |
| run: make test | |
| ubuntu_20: | |
| name: Ubuntu 20 | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: install packages | |
| run: sudo apt-get update && sudo apt-get install -y zlib1g-dev libhdf5-dev | |
| - name: build | |
| run: autoreconf && ./scripts/install-hts.sh && ./configure && make -j8 | |
| - name: test | |
| run: make test | |
| ubuntu_22: | |
| name: Ubuntu 22 | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - name: install packages | |
| run: sudo apt-get update && sudo apt-get install -y zlib1g-dev | |
| - name: build | |
| run: autoreconf --install && ./scripts/install-hts.sh && ./configure --disable-hdf5 && make -j8 disable_hdf5=1 | |
| - name: test | |
| run: test/test_slow5.sh | |
| ubuntu_14_cuda_6_5: | |
| name: Ubuntu 14 cuda 6.5 | |
| runs-on: ubuntu-20.04 | |
| container: ubuntu:14.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: install packages | |
| run: sudo apt-get update && sudo apt-get install -y zlib1g-dev libhdf5-dev gcc g++ autoconf automake make wget | |
| - name: env | |
| run: lsb_release -a && ldd --version && gcc --version && g++ --version | |
| - name: cuda repo setup | |
| run: wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1404/x86_64/cuda-repo-ubuntu1404_7.0-28_amd64.deb && sudo dpkg -i cuda-repo-ubuntu1404_7.0-28_amd64.deb && sudo apt-get update | |
| - name: cuda install | |
| run: sudo apt-get install -y cuda-core-6-5 cuda-cudart-dev-6-5 | |
| - name: cuda env setup | |
| run: sudo ln -s /usr/local/cuda-6.5/ /usr/local/cuda | |
| - name: build | |
| run: export PATH=/usr/local/cuda/bin:${PATH} && autoreconf && ./scripts/install-hts.sh && ./configure && make cuda=1 -j8 | |
| - name: test | |
| run: make test || scripts/test.sh custom --disable-cuda=yes | |
| os_x_11: | |
| name: OSX 11 | |
| runs-on: macos-11 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: install packages | |
| run: brew install hdf5 autoconf automake | |
| - name: build | |
| run: autoreconf --install && ./scripts/install-hts.sh && ./configure && make -j8 | |
| - name: test | |
| run: make test | |
| os_x_11_2: | |
| name: OSX 11 hdf5 install script | |
| runs-on: macos-11 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: install packages | |
| run: brew install hdf5 autoconf automake | |
| - name: build | |
| run: autoreconf --install && CC=gcc CXX=g++ CFLAGS="-Wno-implicit-function-declaration" ./scripts/install-hdf5.sh && ./scripts/install-hts.sh && ./configure --enable-localhdf5 && make -j8 | |
| - name: test | |
| run: make test | |
| ubuntu_arm: | |
| name: ubuntu arm | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: docker run --rm --privileged multiarch/qemu-user-static:register --reset | |
| - uses: docker://multiarch/ubuntu-core:arm64-bionic | |
| with: | |
| args: 'uname -a' | |
| - uses: actions/checkout@v1 | |
| - uses: docker://multiarch/ubuntu-core:arm64-bionic | |
| with: | |
| args: > | |
| bash -c "apt-get update && | |
| apt-get install -y zlib1g-dev libhdf5-dev gcc g++ autoconf automake make wget && | |
| ldd --version && gcc --version && g++ --version && | |
| autoreconf && | |
| ./scripts/install-hts.sh && | |
| ./configure && | |
| make -j8 && | |
| make test" |