<commit_before>language: python
python:
    - 2.7.8
    - 2.7
    - pypy
    - 3.3
    - 3.4
    - 3.5
    - nightly
    - pypy3

before_install:
    - git clone https://github.com/samtools/htslib.git
    - sudo make -C htslib
    - git clone https://github.com/samtools/samtools.git
    - sudo make -C samtools
    - sudo cp samtools/samtools $HOME/bin
    - sudo cp samtools/misc/wgsim $HOME/bin
    - git clone https://github.com/samtools/bcftools.git
    - sudo make -C bcftools
    - sudo cp bcftools/bcftools $HOME/bin
    - git clone https://github.com/lh3/bwa.git
    - sudo make -C bwa
    - sudo cp bwa/bwa $HOME/bin
    - wget https://github.com/broadinstitute/picard/releases/download/1.131/picard-tools-1.131.zip
    - unzip picard-tools-1.131.zip
#    - wget http://ftp.gnu.org/gnu/automake/automake-1.4.tar.gz
#    - tar -xvf automake-1.4.tar.gz
#    - cd automake-1.4
#    - sudo ./configure && make && make install
#    - cd ..
#    - git clone https://github.com/adamewing/exonerate.git
#    - cd exonerate
#    - sudo ./configure && make && make install
#    - cd ..
    - wget http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0-x86_64.tar.gz
    - tar -xvf exonerate-2.2.0-x86_64.tar.gz
    - sudo cp exonerate-2.2.0-x86_64/bin/* $HOME/bin
    - sudo cp -rf exonerate-2.2.0-x86_64/share/* $HOME/share
    - wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
    - tar xvzf velvet_1.2.10.tgz
    - sudo make -C velvet_1.2.10
    - sudo cp velvet_1.2.10/velvetg $HOME/bin
    - sudo cp velvet_1.2.10/velveth $HOME/bin
    - sudo pip install cython
    - sudo pip install pysam

install: true
script:
    # Get out of the source directory before running tests to avoid PYTHONPATH
    # confusion.  This is necessary to ensure that the speedups module can
    # be found in the installation directory.
    - cd bamsurgeon
    # Copy the coveragerc down so coverage.py can find it.
    - python setup.py build
    - python setup.py install<commit_msg>Update .travis.yml<commit_after>language: python
python:
    - 2.7.8
    - 2.7
    - pypy
    - 3.3
    - 3.4
    - 3.5
    - nightly
    - pypy3

before_install:
    - git clone https://github.com/samtools/htslib.git
    - sudo make -C htslib
    - git clone https://github.com/samtools/samtools.git
    - sudo make -C samtools
    - sudo cp samtools/samtools $HOME/bin
    - sudo cp samtools/misc/wgsim $HOME/bin
    - git clone https://github.com/samtools/bcftools.git
    - sudo make -C bcftools
    - sudo cp bcftools/bcftools $HOME/bin
    - git clone https://github.com/lh3/bwa.git
    - sudo make -C bwa
    - sudo cp bwa/bwa $HOME/bin
    - wget https://github.com/broadinstitute/picard/releases/download/1.131/picard-tools-1.131.zip
    - unzip picard-tools-1.131.zip
#    - wget http://ftp.gnu.org/gnu/automake/automake-1.4.tar.gz
#    - tar -xvf automake-1.4.tar.gz
#    - cd automake-1.4
#    - sudo ./configure && make && make install
#    - cd ..
#    - git clone https://github.com/adamewing/exonerate.git
#    - cd exonerate
#    - sudo ./configure && make && make install
#    - cd ..
    - wget http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0-x86_64.tar.gz
    - tar -xvf exonerate-2.2.0-x86_64.tar.gz
    - sudo cp -rf exonerate-2.2.0-x86_64/* $HOME
#    - sudo cp -rf exonerate-2.2.0-x86_64/share/* $HOME/share
    - wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
    - tar xvzf velvet_1.2.10.tgz
    - sudo make -C velvet_1.2.10
    - sudo cp velvet_1.2.10/velvetg $HOME/bin
    - sudo cp velvet_1.2.10/velveth $HOME/bin
    - sudo pip install cython
    - sudo pip install pysam

install: true
script:
    # Get out of the source directory before running tests to avoid PYTHONPATH
    # confusion.  This is necessary to ensure that the speedups module can
    # be found in the installation directory.
    - cd bamsurgeon
    # Copy the coveragerc down so coverage.py can find it.
    - python setup.py build
    - python setup.py install
{'fraction_non_alphanumeric': 0.1281795511221945, 'fraction_numerical': 0.03940149625935162, 'mean_word_length': 2.163249211356467, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 14, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6734922', 'n_tokens_mistral': 1654, 'n_tokens_neox': 1517, 'n_words': 345}