add assertion to count signal samples and fix wrong insertion at the begnning of ss string #203
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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" |