.travis.yml

sudo: true
dist: xenial
language: bash
before_install:
  - export PATH=$PATH:./nanopolish:./minimap2-2.17_x64-linux
  - wget https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_3.2.1-1~xenial_amd64.deb && sudo apt install ./ont_guppy_cpu_3.2.1-1~xenial_amd64.deb

  # per https://askubuntu.com/a/863986
  - sudo chown -R _apt:root /var/lib/update-notifier/package-data-downloads/partial
  - sudo rm -f /var/lib/update-notifier/package-data-downloads/partial/*.FAILED
  - sudo apt install --reinstall ./ont_guppy_cpu_3.2.1-1~xenial_amd64.deb

  - guppy_basecaller # ensure it works
  - curl -L https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2 | tar -jxvf -
  #- git clone --recursive https://github.com/jts/nanopolish.git && ( cd nanopolish && git checkout v0.11.1 && make)
  #- wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_2.2.2-1~xenial_amd64.deb && dpkg -i --ignore-depends=nvidia-384,libcuda1-384 ont_guppy_2.2.2-2~xenial_amd64.deb
addons:
  apt:
    sources:
    - sourceline: 'ppa:duggan/bats'
    #- sourceline: 'deb http://mirror.oxfordnanoportal.com/apt xenial-stable non-free'
    packages:
    - bats
    - realpath
    - samtools
    - tabix
    - ncbi-blast+
    - gcc
    - libeigen3-dev
    - libhdf5-dev
    - libhdf5-cpp-11
    - libc6
    - libcurl4-openssl-dev
    - libzmq5
    - libboost-atomic1.58.0
    - libboost-chrono1.58.0
    - libboost-date-time1.58.0
    - libboost-filesystem1.58.0
    - libboost-iostreams1.58.0
    - libboost-log1.58.0
  homebrew:
    taps: brewsci/bio
    casks:
      - wtdbg2
      - nanopolish

script: 
  - make
  # basecalling can take a lot of time if only two cpus.
  # Explicitly have stdout being sent to the screen so that travis waits.
  - travis_wait 120 bash scripts/np_basecall-demux_guppy.sh t/vanilla.project t/data/SalmonellaLitchfield.FAST5
  # `make test` should test the output of the raw command.
  - make test