|
1 | | -steps: |
2 | | - - bash: | |
3 | | - set -e pipefail |
4 | | -
|
5 | | - # Install htslib dependencies |
6 | | - if [[ "$AGENT_OS" == "Linux" ]]; then |
7 | | - sudo apt-get update && sudo apt-get install -y automake autoconf libbz2-dev liblzma-dev |
8 | | - fi |
9 | | -
|
10 | | - # Install bcftools (only required for running the CLI tests) |
11 | | - version=1.16 |
12 | | - if [[ "$AGENT_OS" == "Linux" ]]; then |
13 | | - pushd /tmp |
14 | | - wget https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2 |
15 | | - tar xfj bcftools-${version}.tar.bz2 |
16 | | - cd bcftools-${version} |
17 | | - ./configure --prefix=/usr |
18 | | - make -j2 |
19 | | - sudo make install |
20 | | - popd |
21 | | - else |
22 | | - brew install bcftools automake |
23 | | - fi |
24 | | -
|
25 | | - # Install some extra dependencies to speed up the core TileDB build |
26 | | - if [[ "$AGENT_OS" == "Linux" ]]; then |
27 | | - sudo apt-get install -y libssl-dev libbz2-dev liblz4-dev libtbb-dev libcurl4-openssl-dev zlib1g-dev |
28 | | - fi |
29 | | - displayName: 'Install dependencies' |
30 | | -
|
31 | | - - bash: | |
32 | | - # azure bash does not treat intermediate failure as error |
33 | | - # https://github.com/Microsoft/azure-pipelines-yaml/issues/135 |
34 | | - set -e pipefail |
35 | | -
|
36 | | - # Azure sets "SYSTEM=build" for unknown reasons, which breaks the OpenSSL configure script (in TileDB itself) |
37 | | - # - openssl configure uses ENV{SYSTEM} if available: |
38 | | - # https://github.com/openssl/openssl/blob/6d745d740d37d680ff696486218b650512bbbbc6/config#L56 |
39 | | - # - error description: |
40 | | - # https://developercommunity.visualstudio.com/content/problem/602584/openssl-build-error-when-using-pipelines.htm |
41 | | - unset SYSTEM |
42 | | -
|
43 | | - # Configure and build TileDB-VCF |
44 | | - mkdir -p $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build |
45 | | - cd $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build |
46 | | - cmake -DCMAKE_INSTALL_PREFIX=$BUILD_REPOSITORY_LOCALPATH/dist .. |
47 | | -
|
48 | | - make -j4 all tiledb_vcf_unit |
49 | | -
|
50 | | - make install |
51 | | -
|
52 | | - displayName: 'Build and test TileDB-VCF' |
53 | | -
|
54 | | - - bash: | |
55 | | - set -e pipefail |
56 | | - pushd $BUILD_REPOSITORY_LOCALPATH/apis/java |
57 | | -
|
58 | | - ./gradlew assemble |
59 | | -
|
60 | | - export LD_LIBRARY_PATH=$BUILD_REPOSITORY_LOCALPATH/apis/java/build/resources/main/lib:$LD_LIBRARY_PATH |
61 | | -
|
62 | | - displayName: 'Build and test TileDB-VCF Java API' |
63 | | -
|
64 | | - - bash: | |
65 | | - echo "Testing" |
66 | | - ls |
67 | | - echo "listing JNI" |
68 | | - ls $BUILD_REPOSITORY_LOCALPATH/dist/lib |
69 | | -
|
70 | | - echo "listing 2" |
71 | | - ls $BUILD_REPOSITORY_LOCALPATH/apis/java/build/install/lib |
72 | | -
|
73 | | -
|
74 | | - if [[ ( "$AGENT_OS" == "Linux" ) ]]; then |
75 | | - cp $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build/externals/install/lib/*.so* $BUILD_BINARIESDIRECTORY |
76 | | - cp $BUILD_REPOSITORY_LOCALPATH/dist/lib/*.so* $BUILD_BINARIESDIRECTORY |
77 | | - cp $BUILD_REPOSITORY_LOCALPATH/apis/java/build/install/lib/*.so* $BUILD_BINARIESDIRECTORY |
78 | | - fi |
79 | | -
|
80 | | - if [[ ( "$AGENT_OS" == "Darwin" ) ]]; then |
81 | | - cp $BUILD_REPOSITORY_LOCALPATH/dist/lib/*.dylib $BUILD_BINARIESDIRECTORY |
82 | | - cp $BUILD_REPOSITORY_LOCALPATH/apis/java/build/install/lib/*.dylib $BUILD_BINARIESDIRECTORY |
83 | | - fi |
84 | | -
|
85 | | - displayName: 'Test' |
86 | | -
|
87 | | - - script: | |
88 | | - echo $sourceVersion |
89 | | - commitHash=${sourceVersion:0:7} |
90 | | - echo $commitHash |
91 | | - echo "##vso[task.setvariable variable=commitHash]$commitHash" ## Set variable for using in other tasks. |
92 | | - env: { sourceVersion: $(Build.SourceVersion) } |
93 | | - displayName: Git Hash 7-digit |
94 | | -
|
95 | | - - bash: | |
96 | | - git describe --tags > $BUILD_REPOSITORY_LOCALPATH/version.txt |
97 | | - displayName: 'Capture version' |
98 | | -
|
99 | | - - task: ArchiveFiles@2 |
100 | | - inputs: |
101 | | - rootFolderOrFile: '$(Build.BinariesDirectory)' |
102 | | - includeRootFolder: false |
103 | | - archiveType: 'tar' # Options: zip, 7z, tar, wim |
104 | | - tarCompression: 'gz' # Optional. Options: gz, bz2, xz, none |
105 | | - archiveFile: $(Build.ArtifactStagingDirectory)/tiledb-vcf-$(Agent.OS)-$(Build.SourceBranchName)-$(commitHash).tar.gz |
106 | | - replaceExistingArchive: true |
107 | | - verbose: true # Optional |
108 | | - condition: succeeded() |
109 | | - |
110 | | - - task: PublishBuildArtifacts@1 |
111 | | - inputs: |
112 | | - pathtoPublish: $(Build.ArtifactStagingDirectory)/tiledb-vcf-$(Agent.OS)-$(Build.SourceBranchName)-$(commitHash).tar.gz |
113 | | - artifactName: libraries |
114 | | - condition: succeeded() |
115 | | - |
116 | | - - bash: | |
117 | | - set -e pipefail |
118 | | - # Display log files if the build failed |
119 | | - echo "Dumping log files for failed build" |
120 | | - echo "----------------------------------" |
121 | | - for f in $(find $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build -name *.log); |
122 | | - do echo "------" |
123 | | - echo $f |
124 | | - echo "======" |
125 | | - cat $f |
126 | | - done; |
127 | | - condition: failed() # only run this job if the build step failed |
128 | | - displayName: "Print log files (failed build only)" |
0 commit comments