.travis.yml

language: perl

sudo: false

perl:
    - "5.26"

env:
  - BLASTVER=2.9.0 CACHEDIR=tarballs

cache:
  directories:
    - $CACHEDIR

install:
    - "cpanm --quiet --notest Moo JSON List::MoreUtils"
    - "mkdir -p $CACHEDIR"
    - "wget -N -c -P $CACHEDIR http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLASTVER}/ncbi-blast-${BLASTVER}+-x64-linux.tar.gz"
    - "tar zxvf $CACHEDIR/ncbi-blast-${BLASTVER}+-x64-linux.tar.gz"
    - "curl https://raw.githubusercontent.com/tseemann/any2fasta/master/any2fasta > bin/any2fasta"
    - "chmod +x bin/any2fasta"
    - "export PATH=$PWD/bin:$PWD/ncbi-blast-${BLASTVER}+/bin:$PATH"

script:
    - "mlst --check"
    - "mlst --version"
    - "mlst --help"
    - "! mlst --doesnotexist"
    - "! mlst -q /etc"
    - "! mlst -q /etc/shadow"
    - "mlst --list | grep saureus"
    - "mlst --longlist | grep saureus"
    - "mlst -q test/example.fna.gz | grep -w 184"
    - "mlst -q test/example.gbk.gz | grep -w 184"
    - "mlst -q test/novel.fasta.bz2 | grep -w spneumoniae"
    - "gzip -d -c test/example.fna.gz | mlst -q /dev/stdin | grep -w 184"
    - "gzip -d -c test/example.gbk.gz | mlst -q /dev/stdin | grep -w 184"
    - "mlst -q --legacy --scheme sepidermidis test/example.fna.gz test/example.gbk.gz"
    - "mlst -q --csv test/example.fna.gz | grep ',184,'"
    - "mlst -q test/example.gbk.gz --json out.json && grep 'sequence_type' out.json"
    - "! mlst -q --label double_trouble test/example.gbk.gz test/example.fna.gz"
    - "mlst -q --label GDAYMATE test/example.fna.gz | grep GDAYMATE"
    - "mlst -q --novel novel.fa test/novel.fasta.bz2 && grep 'recP' novel.fa"
    - "scripts/mlst-show_seqs -s efaecium -t 111"