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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,128 +0,0 @@ | ||
| steps: | ||
| - bash: | | ||
| set -e pipefail | ||
| # Install htslib dependencies | ||
| if [[ "$AGENT_OS" == "Linux" ]]; then | ||
| sudo apt-get update && sudo apt-get install -y automake autoconf libbz2-dev liblzma-dev | ||
| fi | ||
| # Install bcftools (only required for running the CLI tests) | ||
| version=1.16 | ||
| if [[ "$AGENT_OS" == "Linux" ]]; then | ||
| pushd /tmp | ||
| wget https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2 | ||
| tar xfj bcftools-${version}.tar.bz2 | ||
| cd bcftools-${version} | ||
| ./configure --prefix=/usr | ||
| make -j2 | ||
| sudo make install | ||
| popd | ||
| else | ||
| brew install bcftools automake | ||
| fi | ||
| # Install some extra dependencies to speed up the core TileDB build | ||
| if [[ "$AGENT_OS" == "Linux" ]]; then | ||
| sudo apt-get install -y libssl-dev libbz2-dev liblz4-dev libtbb-dev libcurl4-openssl-dev zlib1g-dev | ||
| fi | ||
| displayName: 'Install dependencies' | ||
| - bash: | | ||
| # azure bash does not treat intermediate failure as error | ||
| # https://github.com/Microsoft/azure-pipelines-yaml/issues/135 | ||
| set -e pipefail | ||
| # Azure sets "SYSTEM=build" for unknown reasons, which breaks the OpenSSL configure script (in TileDB itself) | ||
| # - openssl configure uses ENV{SYSTEM} if available: | ||
| # https://github.com/openssl/openssl/blob/6d745d740d37d680ff696486218b650512bbbbc6/config#L56 | ||
| # - error description: | ||
| # https://developercommunity.visualstudio.com/content/problem/602584/openssl-build-error-when-using-pipelines.htm | ||
| unset SYSTEM | ||
| # Configure and build TileDB-VCF | ||
| mkdir -p $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build | ||
| cd $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build | ||
| cmake -DCMAKE_INSTALL_PREFIX=$BUILD_REPOSITORY_LOCALPATH/dist .. | ||
| make -j4 all tiledb_vcf_unit | ||
| make install | ||
| displayName: 'Build and test TileDB-VCF' | ||
| - bash: | | ||
| set -e pipefail | ||
| pushd $BUILD_REPOSITORY_LOCALPATH/apis/java | ||
| ./gradlew assemble | ||
| export LD_LIBRARY_PATH=$BUILD_REPOSITORY_LOCALPATH/apis/java/build/resources/main/lib:$LD_LIBRARY_PATH | ||
| displayName: 'Build and test TileDB-VCF Java API' | ||
| - bash: | | ||
| echo "Testing" | ||
| ls | ||
| echo "listing JNI" | ||
| ls $BUILD_REPOSITORY_LOCALPATH/dist/lib | ||
| echo "listing 2" | ||
| ls $BUILD_REPOSITORY_LOCALPATH/apis/java/build/install/lib | ||
| if [[ ( "$AGENT_OS" == "Linux" ) ]]; then | ||
| cp $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build/externals/install/lib/*.so* $BUILD_BINARIESDIRECTORY | ||
| cp $BUILD_REPOSITORY_LOCALPATH/dist/lib/*.so* $BUILD_BINARIESDIRECTORY | ||
| cp $BUILD_REPOSITORY_LOCALPATH/apis/java/build/install/lib/*.so* $BUILD_BINARIESDIRECTORY | ||
| fi | ||
| if [[ ( "$AGENT_OS" == "Darwin" ) ]]; then | ||
| cp $BUILD_REPOSITORY_LOCALPATH/dist/lib/*.dylib $BUILD_BINARIESDIRECTORY | ||
| cp $BUILD_REPOSITORY_LOCALPATH/apis/java/build/install/lib/*.dylib $BUILD_BINARIESDIRECTORY | ||
| fi | ||
| displayName: 'Test' | ||
| - script: | | ||
| echo $sourceVersion | ||
| commitHash=${sourceVersion:0:7} | ||
| echo $commitHash | ||
| echo "##vso[task.setvariable variable=commitHash]$commitHash" ## Set variable for using in other tasks. | ||
| env: { sourceVersion: $(Build.SourceVersion) } | ||
| displayName: Git Hash 7-digit | ||
| - bash: | | ||
| git describe --tags > $BUILD_REPOSITORY_LOCALPATH/version.txt | ||
| displayName: 'Capture version' | ||
| - task: ArchiveFiles@2 | ||
| inputs: | ||
| rootFolderOrFile: '$(Build.BinariesDirectory)' | ||
| includeRootFolder: false | ||
| archiveType: 'tar' # Options: zip, 7z, tar, wim | ||
| tarCompression: 'gz' # Optional. Options: gz, bz2, xz, none | ||
| archiveFile: $(Build.ArtifactStagingDirectory)/tiledb-vcf-$(Agent.OS)-$(Build.SourceBranchName)-$(commitHash).tar.gz | ||
| replaceExistingArchive: true | ||
| verbose: true # Optional | ||
| condition: succeeded() | ||
|
|
||
| - task: PublishBuildArtifacts@1 | ||
| inputs: | ||
| pathtoPublish: $(Build.ArtifactStagingDirectory)/tiledb-vcf-$(Agent.OS)-$(Build.SourceBranchName)-$(commitHash).tar.gz | ||
| artifactName: libraries | ||
| condition: succeeded() | ||
|
|
||
| - bash: | | ||
| set -e pipefail | ||
| # Display log files if the build failed | ||
| echo "Dumping log files for failed build" | ||
| echo "----------------------------------" | ||
| for f in $(find $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build -name *.log); | ||
| do echo "------" | ||
| echo $f | ||
| echo "======" | ||
| cat $f | ||
| done; | ||
| condition: failed() # only run this job if the build step failed | ||
| displayName: "Print log files (failed build only)" | ||