language: perl

sudo: false

# for threads - https://docs.travis-ci.com/user/languages/perl/

perl:

- "5.18-shrplib"

# velvet default KMER is too small

install:

- "wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz"

- "tar zxf velvet_1.2.10.tgz"

- "make -C velvet_1.2.10 MAXKMERLENGTH=127 OPENMP=1 CATEGORIES=2"

- "export PATH=$PWD:$PWD/velvet_1.2.10:$PATH"

- "export OMP_NUM_THREADS=4"

- "cpanm --quiet --notest Bio::Perl"

before_script:

- "velveth | grep 'MAXKMERLENGTH = 127'"

- "velveth | grep 'OPENMP'"

- "export TD=test/data/test"

script:

- "VelvetOptimiser.pl --help"

- "VelvetOptimiser.pl --version"

- "! VelvetOptimiser.pl --awesomeness"

- "VelvetOptimiser.pl -d out1 -s 55 -e 59 -f '-shortPaired -fastq.gz -separate ${TD}_short_R1.fq.gz ${TD}_short_R2.fq.gz' "

- "grep -c '>NODE' out1/contigs.fa"