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.azure-pipelines.yml
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# Python package
# Create and test a Python package on multiple Python versions.
# Add steps that analyze code, save the dist with the build record, publish to a PyPI-compatible index, and more:
# https://docs.microsoft.com/azure/devops/pipelines/languages/python
trigger:
- master
strategy:
matrix:
linux:
image.name: 'ubuntu-latest'
mac:
image.name: 'macos-latest'
windows:
image.name: 'windows-latest'
pool:
vmImage: $(image.name)
steps:
- task: UsePythonVersion@0
inputs:
versionSpec: '2.7'
addToPath: false
displayName: 'Use Python 2.7'
name: python2
- task: UsePythonVersion@0
inputs:
versionSpec: '3.6'
addToPath: false
displayName: 'Use Python 3.6'
name: python3
# linux
# Python 2.7.16
# /opt/hostedtoolcache/Python/2.7.16/x64/python
# macOS
# Python 2.7.16
# /Users/runner/hostedtoolcache/Python/2.7.16/x64/python
# Windows
# Python 2.7.16
# C:\hostedtoolcache\windows\Python\2.7.16\x64\python.exe
- script: |
$(python2.pythonLocation)/python --version
$(python2.pythonLocation)/python -c "import sys; print(sys.executable)"
displayName: Show version and location of 'python2' binary
# linux
# Python 3.6.9
# /opt/hostedtoolcache/Python/3.6.9/x64/python
# macOS
# Python 3.6.9
# /Users/runner/hostedtoolcache/Python/3.6.9/x64/python
# Windows
# Python 3.6.8
# C:\hostedtoolcache\windows\Python\3.6.8\x64\python.exe
- script: |
$(python3.pythonLocation)/python --version
$(python3.pythonLocation)/python -c "import sys; print(sys.executable)"
displayName: Show version and location of 'python3' binary
#### Begin CONDA ####
# Linux
- bash: |
echo "##vso[task.prependpath]$CONDA/bin"
condition: eq( variables['Agent.OS'], 'Linux' )
displayName: Install 'conda' dependencies on Linux
# macOS
# On Hosted macOS, the agent user doesn't have ownership of Miniconda's installation directory/
# We need to take ownership if we want to update conda or install packages globally
# Take ownership of conda installation
#- bash: sudo chown -R $USER $CONDA
- bash: |
echo "##vso[task.prependpath]$CONDA/bin"
condition: eq( variables['Agent.OS'], 'Darwin' )
displayName: Install 'conda' dependencies on macOS
# Windows
- powershell: |
Write-Host "##vso[task.prependpath]$env:CONDA\Scripts"
condition: eq( variables['Agent.OS'], 'Windows_NT' )
displayName: Install 'conda' dependencies on Windows
- script: |
conda info
displayName: Show version of 'conda' binary
#### End CONDA ####
- script: |
$(python3.pythonLocation)/python -m pip install setuptools
$(python3.pythonLocation)/python -m pip install --upgrade pip
$(python3.pythonLocation)/python -m pip install regex
$(python3.pythonLocation)/python -m pip install primer3-py
displayName: Install 'AddTag' dependencies
- script: |
$(python2.pythonLocation)/python -m pip install setuptools
$(python2.pythonLocation)/python -m pip install --upgrade pip
$(python2.pythonLocation)/python -m pip install numpy==1.16.4
$(python2.pythonLocation)/python -m pip install biopython==1.76
$(python2.pythonLocation)/python -m pip install git+https://github.com/MicrosoftResearch/Azimuth.git
displayName: Install 'Azimuth' dependencies
- script: |
$(python3.pythonLocation)/python -m pip install theano==1.0.4 keras==2.2.4
displayName: Install 'DeepCpf1/CINDEL' dependencies
#### Begin BLAST+ ####
# Linux
- bash: |
wget -nv ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz
tar -xf ncbi-blast-2.9.0+-x64-linux.tar.gz
echo "##vso[task.prependpath]$(Build.SourcesDirectory)/ncbi-blast-2.9.0+/bin"
condition: eq( variables['Agent.OS'], 'Linux' )
displayName: Install 'BLAST+' dependencies on Linux
# macOS
# IMAGE=ncbi-blast-2.9.0+
# curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/${IMAGE}.dmg
# sudo hdiutil attach ${IMAGE}.dmg
# sudo installer -package /Volumes/${IMAGE}/${IMAGE}.pkg -target /
# sudo hdiutil detach /Volumes/${IMAGE}
- bash: |
curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-macosx.tar.gz
tar -xf ncbi-blast-2.9.0+-x64-macosx.tar.gz
echo "##vso[task.prependpath]$(Build.SourcesDirectory)/ncbi-blast-2.9.0+/bin"
condition: eq( variables['Agent.OS'], 'Darwin' )
displayName: Install 'BLAST+' dependencies on macOS
# Windows
# $env:PATH += "$(Build.SourcesDirectory)\ncbi-blast-2.9.0+\bin;"
- powershell: |
(New-Object System.Net.WebClient).DownloadFile("ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-win64.tar.gz","ncbi-blast-2.9.0+-x64-win64.tar.gz")
7z.exe x .\ncbi-blast-2.9.0+-x64-win64.tar.gz
7z.exe x .\ncbi-blast-2.9.0+-x64-win64.tar
echo "##vso[task.prependpath]$(Build.SourcesDirectory)\ncbi-blast-2.9.0+\bin"
condition: eq( variables['Agent.OS'], 'Windows_NT' )
displayName: Install 'BLAST+' dependencies on Windows
- script: |
blastn -version
displayName: Show version of 'blastn' binary
#### End BLAST+ ####
#### Begin MAFFT ####
# To install this package with 'conda' run the following (Linux and macOS):
# conda install -c bioconda mafft
- bash: |
wget -nv https://mafft.cbrc.jp/alignment/software/mafft-7.467-linux.tgz
tar -xf mafft-7.467-linux.tgz
echo "##vso[task.prependpath]$(Build.SourcesDirectory)/mafft-linux64/mafftdir/bin"
echo "##vso[task.setvariable variable=MAFFT_BINARIES]$(Build.SourcesDirectory)/mafft-linux64/mafftdir/libexec"
echo "##vso[task.setvariable variable=MAFFT]mafft"
condition: eq( variables['Agent.OS'], 'Linux' )
displayName: Install 'MAFFT' dependencies on Linux
- bash: |
curl -O https://mafft.cbrc.jp/alignment/software/mafft-7.467-mac.zip
unzip mafft-7.467-mac.zip
echo "##vso[task.prependpath]$(Build.SourcesDirectory)/mafft-mac/mafftdir/bin"
echo "##vso[task.setvariable variable=MAFFT_BINARIES]$(Build.SourcesDirectory)/mafft-mac/mafftdir/libexec"
echo "##vso[task.setvariable variable=MAFFT]mafft"
condition: eq( variables['Agent.OS'], 'Darwin' )
displayName: Install 'MAFFT' dependencies on macOS
- powershell: |
(New-Object System.Net.WebClient).DownloadFile("https://mafft.cbrc.jp/alignment/software/mafft-7.450-win64-signed.zip","mafft-7.450-win64-signed.zip")
7z.exe x .\mafft-7.450-win64-signed.zip
echo "##vso[task.setvariable variable=MAFFT_BINARIES]$(Build.SourcesDirectory)\mafft-win\usr\lib\mafft"
echo "##vso[task.prependpath]$(Build.SourcesDirectory)\mafft-win\usr\bin"
echo "##vso[task.prependpath]$(Build.SourcesDirectory)\mafft-win"
echo "##vso[task.setvariable variable=MAFFT]mafft.bat"
condition: eq( variables['Agent.OS'], 'Windows_NT' )
displayName: Install 'MAFFT' dependencies on Windows
- script: |
echo MAFFT_BINARIES
echo $(MAFFT_BINARIES)
$(MAFFT) --version
displayName: Show version of 'mafft' binary
#### End MAFFT ####
#### Begin BOWTIE2 ####
# To install this package with 'conda' run the following (Linux and macOS):
# conda install -c bioconda bowtie2
- bash: |
wget -nv https://github.com/BenLangmead/bowtie2/releases/download/v2.4.2/bowtie2-2.4.2-linux-x86_64.zip
unzip bowtie2-2.4.2-linux-x86_64.zip
echo "##vso[task.prependpath]$(Build.SourcesDirectory)/bowtie2-2.4.2-linux-x86_64"
echo "##vso[task.setvariable variable=BOWTIE2]bowtie2"
echo "##vso[task.setvariable variable=BOWTIE2_BUILD]bowtie2-build"
condition: eq( variables['Agent.OS'], 'Linux' )
displayName: Install 'BOWTIE2' dependencies on Linux
- bash: |
curl -L -O https://github.com/BenLangmead/bowtie2/releases/download/v2.4.2/bowtie2-2.4.2-macos-x86_64.zip
unzip bowtie2-2.4.2-macos-x86_64.zip
echo "##vso[task.prependpath]$(Build.SourcesDirectory)/bowtie2-2.4.2-macos-x86_64"
echo "##vso[task.setvariable variable=BOWTIE2]bowtie2"
echo "##vso[task.setvariable variable=BOWTIE2_BUILD]bowtie2-build"
condition: eq( variables['Agent.OS'], 'Darwin' )
displayName: Install 'BOWTIE2' dependencies on macOS
- powershell: |
(New-Object System.Net.WebClient).DownloadFile("https://github.com/BenLangmead/bowtie2/releases/download/v2.3.4.3/bowtie2-2.3.4.3-mingw-x86_64.zip","bowtie2-2.3.4.3-mingw-x86_64.zip")
7z.exe x .\bowtie2-2.3.4.3-mingw-x86_64.zip
echo "##vso[task.prependpath]$(Build.SourcesDirectory)\bowtie2-2.3.4.3-mingw-x86_64"
echo "##vso[task.setvariable variable=BOWTIE2]bowtie2.bat"
echo "##vso[task.setvariable variable=BOWTIE2_BUILD]bowtie2-build.bat"
New-Item -Name strawberry-perl -ItemType directory
(New-Object System.Net.WebClient).DownloadFile("http://strawberryperl.com/download/5.30.2.1/strawberry-perl-5.30.2.1-64bit-portable.zip","strawberry-perl-5.30.2.1-64bit-portable.zip")
7z.exe x .\strawberry-perl-5.30.2.1-64bit-portable.zip -ostrawberry-perl
echo "##vso[task.prependpath]$(Build.SourcesDirectory)\strawberry-perl\perl\bin"
#echo "##vso[task.prependpath]$(Build.SourcesDirectory)\strawberry-perl\c\bin"
#echo "##vso[task.prependpath]$(Build.SourcesDirectory)\strawberry-perl\perl\site\bin"
echo "##vso[task.prependpath]$(python2.pythonLocation)"
condition: eq( variables['Agent.OS'], 'Windows_NT' )
displayName: Install 'BOWTIE2' dependencies on Windows
- script: |
$(BOWTIE2) --version
$(BOWTIE2_BUILD) --version
displayName: Show version of 'bowtie2' binaries
#### End BOWTIE2 ####
#### Begin CAS-OFFINDER ####
- bash: |
mkdir cas-offinder-2.4
cd cas-offinder-2.4/
wget -nv https://versaweb.dl.sourceforge.net/project/cas-offinder/Binaries/2.4/Linux64/cas-offinder
echo "##vso[task.prependpath]$(Build.SourcesDirectory)/cas-offinder-2.4"
condition: False # eq( variables['Agent.OS'], 'Linux' )
displayName: Install 'CAS-OFFINDER' dependencies on Linux
- bash: |
mkdir cas-offinder-2.4
cd cas-offinder-2.4/
curl -O https://phoenixnap.dl.sourceforge.net/project/cas-offinder/Binaries/2.4/Mac/cas-offinder
echo "##vso[task.prependpath]$(Build.SourcesDirectory)/cas-offinder-2.4"
condition: False # eq( variables['Agent.OS'], 'Darwin' )
displayName: Install 'CAS-OFFINDER' dependencies on macOS
- powershell: |
New-Item -Name cas-offinder-2.4 -ItemType directory
Invoke-WebRequest -Uri https://versaweb.dl.sourceforge.net/project/cas-offinder/Binaries/2.4/Win64/cas-offinder.exe -OutFile cas-offinder-2.4\cas-offinder.exe -UserAgent NativeHost
echo "##vso[task.prependpath]$(Build.SourcesDirectory)\cas-offinder-2.4"
condition: False # eq( variables['Agent.OS'], 'Windows_NT' )
displayName: Install 'CAS-OFFINDER' dependencies on Windows
- script: |
cas-offinder
condition: False
displayName: Show version of 'cas-offinder' binary
#### End CAS-OFFINDER ####
- script: |
$(python3.pythonLocation)/python -m pip install pytest pytest-azurepipelines pytest-cov
$(python3.pythonLocation)/python -m pytest --cov source --cov-report xml --cov-report html tests/
displayName: PyTest
- script: |
pwd
cd $(Build.SourcesDirectory)
pwd
cd $(System.DefaultWorkingDirectory)
pwd
displayName: Show values of built-in pipeline paths
- script: |
$(python3.pythonLocation)/python addtag --help
displayName: Usage
- task: PublishCodeCoverageResults@1
inputs:
codeCoverageTool: Cobertura
summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov'
displayName: 'Publish code coverage results'