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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"
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