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Linux x86_64

fix workflows #233

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fix workflows

fix workflows #233

Workflow file for this run

.github/workflows/f5c-x86_64.yml at ddbfc6c
name: Linux x86_64
on:
push:
branches: '**'
pull_request:
branches: '**'
env:
ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
jobs:
ubuntu_14_local_hts:
name: ubuntu 14 local hts
runs-on: ubuntu-20.04
container:
image: ubuntu:14.04
volumes:
- /node20217:/node20217:rw,rshared
- /node20217:/__e/node20:ro,rshared
steps:
- name: nodejs
run: |
apt-get update && apt-get install -y wget xz-utils
wget https://unofficial-builds.nodejs.org/download/release/v20.9.0/node-v20.9.0-linux-x64-glibc-217.tar.xz
tar -xf node-v20.9.0-linux-x64-glibc-217.tar.xz --strip-components 1 -C /node20217
- 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:
image: ubuntu:16.04
volumes:
- /node20217:/node20217:rw,rshared
- /node20217:/__e/node20:ro,rshared
steps:
- name: nodejs
run: |
apt-get update && apt-get install -y wget xz-utils
wget https://unofficial-builds.nodejs.org/download/release/v20.9.0/node-v20.9.0-linux-x64-glibc-217.tar.xz
tar -xf node-v20.9.0-linux-x64-glibc-217.tar.xz --strip-components 1 -C /node20217
- 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:
image: ubuntu:16.04
volumes:
- /node20217:/node20217:rw,rshared
- /node20217:/__e/node20:ro,rshared
steps:
- name: nodejs
run: |
apt-get update && apt-get install -y wget xz-utils
wget https://unofficial-builds.nodejs.org/download/release/v20.9.0/node-v20.9.0-linux-x64-glibc-217.tar.xz
tar -xf node-v20.9.0-linux-x64-glibc-217.tar.xz --strip-components 1 -C /node20217
- 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:
image: ubuntu:18.04
volumes:
- /node20217:/node20217:rw,rshared
- /node20217:/__e/node20:ro,rshared
steps:
- name: nodejs
run: |
apt-get update && apt-get install -y wget xz-utils
wget https://unofficial-builds.nodejs.org/download/release/v20.9.0/node-v20.9.0-linux-x64-glibc-217.tar.xz
tar -xf node-v20.9.0-linux-x64-glibc-217.tar.xz --strip-components 1 -C /node20217
- 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_24:
name: Ubuntu 24
runs-on: ubuntu-24.04
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:
image: ubuntu:14.04
volumes:
- /node20217:/node20217:rw,rshared
- /node20217:/__e/node20:ro,rshared
steps:
- name: nodejs
run: |
apt-get update && apt-get install -y wget xz-utils
wget https://unofficial-builds.nodejs.org/download/release/v20.9.0/node-v20.9.0-linux-x64-glibc-217.tar.xz
tar -xf node-v20.9.0-linux-x64-glibc-217.tar.xz --strip-components 1 -C /node20217
- 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_13:
name: OSX 13
runs-on: macos-13
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_13_2:
name: OSX 13 hdf5 install script
runs-on: macos-13
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
os_x_14:
name: OSX 14
runs-on: macos-14
steps:
- uses: actions/checkout@v2
- name: install packages
run: brew install hdf5 autoconf automake
- name: build
run: autoreconf --install && ./scripts/install-hts.sh && ./configure --disable-hdf5 && make -j8
- name: test
run: test/test_slow5.sh
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"