language: perl sudo: false addons: apt: packages: - hmmer - bedtools perl: - "5.26" install: - "export PATH=$PWD/bin:$PATH" - "sed -i~ -e 's/-name+/-name/' bin/barrnap" script: - "barrnap --version" - "barrnap --help" - "barrnap --citation" - "! barrnap --doesnotexist" - "barrnap 2>&1 | grep 'ERROR: No input file'" - "barrnap -q --kingdom bac examples/bacteria.fna" - "barrnap -q --kingdom arc examples/bacteria.fna" - "barrnap -q --kingdom mito examples/mitochondria.fna" - "barrnap -q --kingdom euk examples/fungus.fna" - "! barrnap examples/empty.fna" - "! barrnap examples/null.fna" - "barrnap -q examples/small.fna | grep 16S_rRNA" - "barrnap -q < examples/small.fna | grep 16S_rRNA" - "barrnap -q - < examples/small.fna | grep 16S_rRNA" - "barrnap examples/nohits.fna 2>&1 | grep 'Found 0 '" - "barrnap --threads 2 examples/small.fna" - "barrnap -q --incseq examples/small.fna | grep '^>'" - "barrnap -q --outseq hits.fa < examples/small.fna && head -n3 hits.fa"