.travis.yml

language: python

notifications:
  email: true

python:
  - "3.7"

env:
  - BLAST_VERSION=2.14.1

before_install:
  - sudo apt-get -qq update
  - sudo apt-get install -y prodigal
  - sudo apt-get install -y libtbb-dev

  # blast
  - wget http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
  - tar xzf ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
  - sudo mv ncbi-blast-${BLAST_VERSION}+/bin/* /usr/bin

  # bowtie2
  - wget https://github.com/BenLangmead/bowtie2/releases/download/v2.4.5/bowtie2-2.4.5-linux-x86_64.zip
  - unzip bowtie2-2.4.5-linux-x86_64.zip
  - sudo mv bowtie2-2.4.5-linux-x86_64/bowtie2* /usr/bin

  # diamond
  - wget http://github.com/bbuchfink/diamond/releases/download/v0.8.36/diamond-linux64.tar.gz
  - tar xzf diamond-linux64.tar.gz
  - sudo mv diamond /usr/bin

  # samtools
  - wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
  - tar jxf samtools-1.9.tar.bz2
  - pushd samtools-1.9 && ./configure && make && sudo mv samtools /usr/bin && popd

  # bamtools
  - wget https://github.com/pezmaster31/bamtools/archive/v2.5.1.tar.gz
  - tar xzf v2.5.1.tar.gz
  - pushd bamtools-2.5.1/ && mkdir build && cd build && cmake .. && make && sudo make install && popd

  # bedtools
  - wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools
  - chmod +x bedtools && sudo mv bedtools /usr/bin

  # bwa
  - git clone https://github.com/lh3/bwa.git
  - pushd bwa && make && sudo mv bwa /usr/bin && popd

  # jellyfish
  - wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-linux
  - mv jellyfish-linux jellyfish && chmod +x jellyfish && sudo mv jellyfish /usr/bin

  # kma
  - git clone https://bitbucket.org/genomicepidemiology/kma.git
  - pushd kma && make && sudo mv kma /usr/bin && popd

install:
  - pip install -r requirements.txt
  - pip install .

script:
  - ./test.sh