<commit_before>language: python
before-install:
  - sudo add-apt-repository -y ppa:nebc/bio-linux
  - sudo apt-get update 
  - sudo apt-get install -y build-essential bowtie bowtie2 
python:
  - "2.7"
install:
  - sudo apt-add-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`/"
  - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
  - sudo apt-add-repository -y ppa:marutter/c2d4u
  - sudo apt-get update -qq
  - sudo apt-get install -qq r-base-dev r-recommended curl > /dev/null
  # You may want to periodically update this, although the conda update
  # conda line below will keep everything up-to-date.  We do this
  # conditionally because it saves us some downloading if the version is
  # the same.
  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
      wget http://repo.continuum.io/miniconda/Miniconda-3.4.2-Linux-x86_64.sh -O miniconda.sh;
    else
      wget http://repo.continuum.io/miniconda/Miniconda3-3.4.2-Linux-x86_64.sh -O miniconda.sh;
    fi
  - bash miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  # Useful for debugging any issues with conda
  - conda info -a
  - deps='pip jinja2 numpy'
  - deps_doc='pygraphviz sphinx'
  - conda create -p $HOME/py --yes $deps "python=$TRAVIS_PYTHON_VERSION"
  - export PATH=$HOME/py/bin:$PATH
  # python packages not in conda
  - pip install ngs_plumbing enum34 networkx
  # bioconductor packages
  - sudo Rscript -e 'source("http://www.bioconductor.org/biocLite.R"); biocLite(c("edgeR", "limma", "DESeq", "DESeq2"))' > /dev/null
  # 3rd-party bioinformatics tools
  # bowtie2
  - bowtie2_deps='2.2.4'
  - curl -O -J -L http://sourceforge.net/projects/bowtie-bio/files/bowtie2/${bowtie2_deps}/bowtie2-${bowtie2_deps}-linux-x86_64.zip/download
  - unzip bowtie2-${bowtie2_deps}-linux-x86_64.zip
  - export PATH=`pwd`/bowtie2-${bowtie2_deps}:${PATH}
  # samtools
  - curl -O -J -L http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download
  - tar -xjf samtools-0.1.19.tar.bz2
  - cd samtools-0.1.19; make; cd ..
  - export PATH=`pwd`/samtools-0.1.19:${PATH}
  # install railroadtracks
  - python setup.py install
script:
  - python -m railroadtracks.tests<commit_msg>Added BWA (build from source :/) and HTSeq to CI environment<commit_after>language: python
before-install:
  - sudo add-apt-repository -y ppa:nebc/bio-linux
  - sudo apt-get update 
  - sudo apt-get install -y build-essential bowtie bowtie2 
python:
  - "2.7"
install:
  - sudo apt-add-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`/"
  - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
  - sudo apt-add-repository -y ppa:marutter/c2d4u
  - sudo apt-get update -qq
  - sudo apt-get install -qq r-base-dev r-recommended curl > /dev/null
  # You may want to periodically update this, although the conda update
  # conda line below will keep everything up-to-date.  We do this
  # conditionally because it saves us some downloading if the version is
  # the same.
  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
      wget http://repo.continuum.io/miniconda/Miniconda-3.4.2-Linux-x86_64.sh -O miniconda.sh;
    else
      wget http://repo.continuum.io/miniconda/Miniconda3-3.4.2-Linux-x86_64.sh -O miniconda.sh;
    fi
  - bash miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  # Useful for debugging any issues with conda
  - conda info -a
  - deps='pip jinja2 numpy'
  - deps_doc='pygraphviz sphinx'
  - conda create -p $HOME/py --yes $deps "python=$TRAVIS_PYTHON_VERSION"
  - export PATH=$HOME/py/bin:$PATH
  # python packages not in conda
  - pip install ngs_plumbing enum34 networkx
  # bioconductor packages
  - sudo Rscript -e 'source("http://www.bioconductor.org/biocLite.R"); biocLite(c("edgeR", "limma", "DESeq", "DESeq2"))' > /dev/null
  # 3rd-party bioinformatics tools
  # bowtie2
  - bowtie2_deps='2.2.4'
  - curl -O -J -L http://sourceforge.net/projects/bowtie-bio/files/bowtie2/${bowtie2_deps}/bowtie2-${bowtie2_deps}-linux-x86_64.zip/download
  - unzip bowtie2-${bowtie2_deps}-linux-x86_64.zip
  - export PATH=`pwd`/bowtie2-${bowtie2_deps}:${PATH}
  # samtools
  - curl -O -J -L http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download
  - tar -xjf samtools-0.1.19.tar.bz2
  - cd samtools-0.1.19; make; cd ..
  - export PATH=`pwd`/samtools-0.1.19:${PATH}
  # BWA
  - bwa_deps='0.7.10'
  - wget http://downloads.sourceforge.net/project/bio-bwa/bwa-${bwa_deps}.tar.bz2
  - tar -xjf bwa-${bwa_deps}.tar.bz2
  - cd bwa-${bwa_deps}
  - make
  - export PATH=`pwd`:${PATH}
  # HTSeq
  - pip install HTSeq
  # install railroadtracks
  - python setup.py install
script:
  - python -m railroadtracks.tests
{'fraction_non_alphanumeric': 0.14208199356913184, 'fraction_numerical': 0.03135048231511254, 'mean_word_length': 3.1405990016638934, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 7, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '852389', 'n_tokens_mistral': 2091, 'n_tokens_neox': 1939, 'n_words': 428}