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jobs:
- job: ubuntu_1604
pool:
vmImage: 'Ubuntu-16.04'
strategy:
matrix:
python36:
python.version: '3.6'
build.type: 'Debug'
sanitizer: 'ON'
static: 'OFF'
Python27:
python.version: '2.7'
build.type: 'Release'
sanitizer: 'OFF'
static: 'ON'
steps:
- task: UsePythonVersion@0
inputs:
versionSpec: '$(python.version)'
addToPath: true
- script: |
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=$(build.type) -DSANITIZER=$(sanitizer) -DSTATIC_BUILD=$(static) ..
make simple_test -j `nproc`
displayName: 'build and test'
- job: macos
strategy:
matrix:
1013:
image: macos-10.13
latest:
image: macos-latest
pool:
vmImage: $(image)
steps:
- script: |
brew install cmake gcc@9 zlib bzip2
displayName: 'install dependencies'
- script: |
mkdir build
cd build
CC=gcc-9 CXX=g++-9 cmake ..
make simple_test -j `sysctl -n hw.physicalcpu`
displayName: 'build and test'
- job: assembly
timeoutInMinutes: 0
strategy:
matrix:
codecov:
build.type: 'Release'
sanitizer: 'OFF'
coverage: 'ON'
sanitize:
build.type: 'Debug'
sanitizer: 'ON'
coverage: 'OFF'
pool:
vmImage: 'Ubuntu-16.04'
steps:
- script: |
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=$(build.type) -DSANITIZER=$(sanitizer) -DCOVERAGE=$(coverage) ..
make -j `nproc`
make simple_test
sudo make install
displayName: 'build and test'
- script: |
curl -o- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR752/007/SRR7521507/SRR7521507_1.fastq.gz | gzip -cd | head -4000000 | gzip -1 > 1.fq.gz
curl -o- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR752/007/SRR7521507/SRR7521507_2.fastq.gz | gzip -cd | head -4000000 | gzip -1 > 2.fq.gz
megahit --presets meta-large -1 1.fq.gz -2 2.fq.gz -m5e9 --verbose
displayName: 'assemble'
- script: |
if [ $(coverage) = 'ON' ]; then
wget http://downloads.sourceforge.net/ltp/lcov-1.14.tar.gz
tar zvxf lcov-1.14.tar.gz
export PATH=lcov-1.14/bin/:${PATH}
lcov --capture --directory . --output-file coverage.info
lcov --remove coverage.info '/usr/*' --output-file coverage.info # filter system-files
lcov --remove coverage.info '*xxhash/*' --output-file coverage.info # filter xxhash-files
lcov --remove coverage.info '*parallel_hashmap/*' --output-file coverage.info # filter parallel-hashmap-files
lcov --remove coverage.info '*pprintpp/*' --output-file coverage.info # filter pprintpp files
lcov --list coverage.info # debug info
bash <(curl -s https://codecov.io/bash) -f coverage.info -t $(CODECOV_TOKEN) || echo "Codecov did not collect coverage reports"
fi
displayName: 'codecov'
|
