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circle.yml
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circle.yml
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dependencies:
cache_directories:
- "_deps/cmake-3.3.0-Linux-x86_64"
- "_deps/boost_1_58_0"
- "_deps/swig-3.0.8"
pre:
- sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
- sudo apt-get update
- sudo apt-get install g++-4.9
- 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 http://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_58_0 ] ; then wget http://downloads.sourceforge.net/project/boost/boost/1.58.0/boost_1_58_0.tar.bz2 ; tar xjf boost_1_58_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 http://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 $(readlink -f ../../swig-3.0.8) ; make ; make install ; fi
- pushd _deps ; git clone https://github.com/PacificBiosciences/ConsensusCore.git
- pushd _deps ; git clone https://github.com/PacificBiosciences/unanimity.git
- pushd _deps/unanimity; git submodule update --init --remote
- pushd _deps ; git clone https://github.com/PacificBiosciences/PacBioTestData.git
- pip install --upgrade pip
- pip install jsonschema avro requests iso8601
- pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcommand.git
- pip install numpy # deps for pbcore
- pip install cython
- pip install pysam
- pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcore.git
- pip install cram pytest coverage
override:
- pushd _deps/ConsensusCore ; python setup.py install --boost=$(readlink -f ../boost_1_58_0) --swig=$(readlink -f ../swig-3.0.8/bin/swig)
- pushd _deps/unanimity ; CMAKE_BUILD_TYPE=ReleaseWithAssert CC=gcc-4.9 CXX=g++-4.9 CMAKE_COMMAND=$(readlink -f ../cmake-3.3.0-Linux-x86_64/bin/cmake) Boost_INCLUDE_DIRS=$(readlink -f ../boost_1_58_0) SWIG_COMMAND=$(readlink -f ../swig-3.0.8/bin/swig) pip install --verbose --upgrade --no-deps .
- pushd _deps/PacBioTestData ; git lfs pull && make python
test:
pre:
- pip install --verbose --upgrade --no-deps .
override:
- make check