.travis.yml

sudo: required

# services:
#   - docker

language: perl
perl:
  - "5.22"

before_install:
  # - docker pull migun/phame-1 
  - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
  - sudo apt-get update -qq
  # - sudo apt-get -y install -qq gcc-5 g++-5
  # - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 60 --slave /usr/bin/g++ g++ /usr/bin/g++-5

install:
  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
  - chmod +x miniconda.sh
  - ./miniconda.sh -b -f
  - export PATH="/home/travis/miniconda3/bin:$PATH"
  - conda update --yes -n base conda
  - conda config --add channels r
  - conda config --add channels defaults
  - conda config --add channels conda-forge
  - conda config --add channels bioconda
  - conda create --yes -n phame_env
  - conda install --yes -c bioconda phame -n phame_env
  # - conda install --yes -c bioconda samtools>=1.7
  # - conda install --yes -c bioconda bbmap>=37.62
  # - conda install --yes -c bioconda bowtie2=2.3.0
  # - conda install --yes -c bioconda perl-app-cpanminus=1.7039
  # - conda install --yes -c bioconda bcftools
  # - conda install --yes -c bioconda bwa
  # - conda install --yes -c bioconda fasttree
  # - conda install --yes -c bioconda bbmap
  # - conda install --yes -c bioconda raxml
  # - cpanm Getopt::Long@2.45
  # - cpanm Test::Exception@0.43
  # - cpanm Statistics::Distributions@1.02
  # - cpanm File::Path@2.09
  # - cpanm File::Basename@2.85
  # - cpanm File::Copy@2.21
  # - cpanm Parallel::ForkManager@1.17
  # - export PATH="$HOME/build/mshakya/PhaME-1/src:$HOME/build/mshakya/PhaME-1/thirdParty/miniconda/bin:$PATH"

# before_script:
  # - cpanm --quiet --notest --skip-satisfied Devel::Cover::Report::Codecov

script:
  - source activate phame_env
  - test/TestAll.sh 2
  - test/TestAll.sh 7
  # - cover -test
  # - docker run --rm migun/phame-1 sh test/TestAll.sh 

#after_success:
#  - cover -report codecov