.travis.yml

language: perl

perl:
  - "5.24"

addons:
  apt:
    sources:
      - ubuntu-toolchain-r-test
    packages:
      - zlib1g-dev
      - cpanminus
      - libdist-zilla-perl
      - ncbi-blast+

before_install:
  # regular ubuntu packages
  - sudo add-apt-repository main
  - sudo add-apt-repository universe

  # R packages
  - echo "deb https://cloud.r-project.org/bin/linux/ubuntu trusty/" | sudo tee -a /etc/apt/sources.list
  - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9

  # update after package changes
  - sudo apt-get update -qq

  # install conda
  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
    else
      wget https://repo.continuum.io/miniconda/Miniconda3-latest-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

  # Set-up conda channels
  - conda config --add channels defaults
  - conda config --add channels bioconda
  - conda config --add channels conda-forge 

install:
  # Install latest R version
  - sudo apt-get -y install r-base r-base-dev

  # Install STAR with conda
  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION star
  - source activate test-environment

  # Install samtools from the sources
  - git clone https://github.com/samtools/htslib.git
  - git clone https://github.com/samtools/samtools.git
  - pushd samtools && autoheader && autoconf -Wno-syntax && ./configure --prefix=/usr && make -j4 && sudo make install && popd
  
  # Install latest gsnap version (with --gunzip support)
  - wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2018-05-30.tar.gz
  - tar -xzvf gmap-gsnap-2018-05-30.tar.gz
  - pushd gmap-2018-05-30 && ./configure --prefix=/usr && make -j4 && sudo make install && popd
  
  # Install R packages (DESeq2)
  - sudo Rscript install_r_packages.R
  
  # Install dkpl-annot with Dist-zilla and CPAN-minus
  - dzil install --install-command 'cpanm .'

script:
  - dkpl index -g toy/references/GRCh38-chr22.fa.gz -a toy/references/GRCh38-chr22.gff.gz -i test_index
  - dkpl annot -v -i test_index --deg toy/dkpl-run/DEGs.tsv.gz toy/dkpl-run/merged-diff-counts.tsv.gz 
  - dkpl annot -v -i test_index --deg toy/dkpl-run/DEGs.tsv.gz --norm-gene-counts toy/dkpl-run/normalized_counts.tsv --sample-conditions toy/dkpl-run/sample_conditions_full.tsv toy/dkpl-run/merged-diff-counts.tsv.gz
  - dkpl index -g toy/references/GRCh38-chr22.fa.gz -a toy/references/GRCh38-chr22.gff.gz -i test_index_star --star
  - dkpl annot -v -i test_index_star --deg toy/dkpl-run/DEGs.tsv.gz toy/dkpl-run/merged-diff-counts.tsv.gz -o test_STAR