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machine:
python:
version: 2.7.9
dependencies:
cache_directories:
- "_deps/cmake-3.3.0-Linux-x86_64"
- "_deps/boost_1_60_0"
- "_deps/swig-3.0.8"
pre:
- curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash
- sudo apt-get install git-lfs=1.1.0
- if [ ! -d _deps ] ; then mkdir _deps ; fi # Create a directory for dependencies, These are static, cache them.
- pushd _deps ; if [ ! -d cmake-3.3.0-Linux-x86_64 ] ; then wget --no-check-certificate https://www.cmake.org/files/v3.3/cmake-3.3.0-Linux-x86_64.tar.gz ; tar xzf cmake-3.3.0-Linux-x86_64.tar.gz ; fi
- pushd _deps ; if [ ! -d boost_1_60_0 ] ; then wget https://downloads.sourceforge.net/project/boost/boost/1.60.0/boost_1_60_0.tar.bz2 ; tar xjf boost_1_60_0.tar.bz2 ; fi
- pushd _deps ; if [ ! -f swig-3.0.8/bin/swig ] ; then rm -fr swig-3.0.8* ; mkdir dl ; pushd dl ; wget https://downloads.sourceforge.net/project/swig/swig/swig-3.0.8/swig-3.0.8.tar.gz ; tar xzf swig-3.0.8.tar.gz ; pushd swig-3.0.8 ; ./configure --prefix $(readlink -f ../../swig-3.0.8) ; make ; make install ; fi
- pushd _deps ; git clone https://github.com/PacificBiosciences/PacBioTestData.git
- pip install --upgrade pip
- pip install numpy cython h5py pysam cram nose jsonschema avro
- pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcommand.git
- pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcore.git
- pushd _deps/PacBioTestData ; git lfs pull && make python
- mkdir _rev_deps # Create a directory for reverse-dependencies, ie things that depend on us. These are not static, do not cache them.
# Build ConsensusCore
- pushd _deps ; git clone https://github.com/PacificBiosciences/ConsensusCore.git
- pushd _deps/ConsensusCore ; python setup.py install --boost=$(readlink -f ../../_deps/boost_1_60_0) --swig=$(readlink -f ../../_deps/swig-3.0.8/bin/swig)
- pushd _rev_deps ; git clone https://github.com/PacificBiosciences/GenomicConsensus.git
- git submodule update --init --remote
override:
- CMAKE_BUILD_TYPE=ReleaseWithAssert CMAKE_COMMAND=$(readlink -f _deps/cmake-3.3.0-Linux-x86_64/bin/cmake) Boost_INCLUDE_DIRS=$(readlink -f _deps/boost_1_60_0) SWIG_COMMAND=$(readlink -f _deps/swig-3.0.8/bin/swig) VERBOSE=1 pip install --verbose --upgrade --no-deps .
- python -c "import ConsensusCore2 ; print ConsensusCore2.__version__"
- pushd _rev_deps/GenomicConsensus ; pip install --upgrade --no-deps --verbose .
- pushd _rev_deps/GenomicConsensus ; make check # Test GC
test:
pre:
- mkdir _build
- pushd _build ; $(readlink -f ../_deps/cmake-3.3.0-Linux-x86_64/bin/cmake) -DBoost_INCLUDE_DIRS=$(readlink -f ../_deps/boost_1_60_0) -DCMAKE_BUILD_TYPE=ReleaseWithAssert ..
override:
- pushd _build ; make
- pushd _build ; make check
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