File: circle.yml

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pbgenomicconsensus 2.1.0-1
  • links: PTS, VCS
  • area: main
  • in suites: stretch
  • size: 26,604 kB
  • ctags: 702
  • sloc: python: 4,659; makefile: 201; xml: 60; sh: 4
file content (35 lines) | stat: -rw-r--r-- 2,489 bytes parent folder | download
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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++-4.8
        - 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 $(readlink -f ../../swig-3.0.8) ; make ; make install ; fi
        - pushd _deps ; git clone https://github.com/PacificBiosciences/ConsensusCore.git
        - pushd _deps ; git clone https://github.com/PacificBiosciences/ConsensusCore2.git
        - pushd _deps ; git clone https://github.com/PacificBiosciences/PacBioTestData.git
        - pip install --upgrade pip
        - pip install numpy
        - pip install cython
        - pip install h5py
        - pip install pysam
        - pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcommand.git
        - pip install --upgrade --no-deps git+https://github.com/PacificBiosciences/pbcore.git
        - pip install cram nose
    override:
        - pushd _deps/ConsensusCore ; python setup.py install --boost=$(readlink -f ../boost_1_58_0) --swig=$(readlink -f ../swig-3.0.8/bin/swig)
        - pushd _deps/ConsensusCore2 ; CC=gcc-4.8 CXX=g++-4.8 CMAKE_COMMAND=$(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 .
    override:
        - make check