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# Starter pipeline
# Start with a minimal pipeline that you can customize to build and deploy your code.
# Add steps that build, run tests, deploy, and more:
# https://aka.ms/yaml
trigger:
- master
pool:
vmImage: 'Ubuntu-16.04'
strategy:
matrix:
avx2:
SIMD: 'AVX2'
FILENAME: 'mmseqs-static_avx2.tar.gz'
STATIC: 1
MPI: 0
sse:
SIMD: 'SSE4.1'
FILENAME: 'mmseqs-static_sse41.tar.gz'
STATIC: 1
MPI: 0
avx2_mpi:
SIMD: 'AVX2'
STATIC: 0
FILENAME: ''
MPI: 1
steps:
- script: |
sudo apt-get update
sudo apt-get -y install pandoc mpi-default-dev mpi-default-bin texlive-latex-recommended texlive-fonts-extra
displayName: 'Install dependencies'
- script: |
mkdir build
cd build
if [ "${STATIC}" -eq "1" ]; then
cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -DBUILD_SHARED_LIBS=OFF \
-DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc \
-static-libstdc++" -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
-DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} ..
else
cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} ..
fi
make -j $(nproc --all)
displayName: 'Run build'
- script: |
mkdir ~/regression && cd ~/regression
git clone https://bitbucket.org/martin_steinegger/mmseqs-benchmark.git
export TTY=0
export MMSEQS_NUM_THREADS=8
export PATH="$(pwd)/mmseqs-benchmark/:$PATH"
./mmseqs-benchmark/run_regression.sh "${BUILD_SOURCESDIRECTORY}/build/src/mmseqs" ~/regression/results/
displayName: 'Run regression test'
- task: DownloadSecureFile@1
inputs:
secureFile: secretKeyPleaseDontSteal
displayName: 'Get the deploy key'
- script: |
[ ! -z "${FILENAME}" ] || exit 0
mkdir ~/.ssh && mv $DOWNLOADSECUREFILE_SECUREFILEPATH ~/.ssh/id_rsa
chmod 700 ~/.ssh && chmod 600 ~/.ssh/id_rsa
ssh-keyscan -t rsa uniclust.mmseqs.com >> ~/.ssh/known_hosts
ssh codeship@uniclust.mmseqs.com "mkdir -p \"/home/mirdita/repositories/mmseqs-webserver/archive/${BUILD_SOURCEVERSION}\""
mkdir -p ~/mmseqs2.wiki
cd ~/mmseqs2.wiki
git clone https://github.com/soedinglab/MMseqs2.wiki.git .
.pandoc/make-pdf.sh
scp userguide.pdf codeship@uniclust.mmseqs.com:"/home/mirdita/repositories/mmseqs-webserver/archive/${BUILD_SOURCEVERSION}"
cd ${BUILD_SOURCESDIRECTORY}/build
CURR_BUILD="mmseqs2"
mkdir -p ${CURR_BUILD}/bin
mkdir -p ${CURR_BUILD}/util
mkdir -p ${CURR_BUILD}
cp src/mmseqs ${CURR_BUILD}/bin
chmod +x ${CURR_BUILD}/bin/mmseqs
cp ../util/bash-completion.sh ${CURR_BUILD}/util
chmod +x ${CURR_BUILD}/util/bash-completion.sh
cp -r ../LICENCE.md ../README.md ~/mmseqs2.wiki/userguide.pdf ../examples ${CURR_BUILD}
chmod -R g-w,o-w ${CURR_BUILD}
tar czvf ${FILENAME} ${CURR_BUILD}
scp ${FILENAME} codeship@uniclust.mmseqs.com:"/home/mirdita/repositories/mmseqs-webserver/archive/${BUILD_SOURCEVERSION}"
ssh codeship@uniclust.mmseqs.com "update-latest-mmseqs.sh \"${BUILD_SOURCEVERSION}\""
displayName: 'Upload build'
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