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|
name: CI
on:
push:
branches: [ master ]
pull_request:
branches: [ master ]
jobs:
build:
runs-on: ubuntu-latest
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v5
- uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: barrnap
environment-file: environment.yml
miniforge-version: latest
channels: conda-forge,bioconda
channel-priority: strict
auto-update-conda: true
- name: Add to PATH
run: echo "${{ github.workspace }}/bin" >> $GITHUB_PATH
- name: Run test
run: barrnap --version
- name: Run test
run: barrnap --help
- name: Run test
run: barrnap --citation
# - name: Run test
# run: barrnap 2>&1 | grep 'ERROR: No input file'
- name: Run test
run: barrnap -q --kingdom bac examples/bacteria.fna
- name: Run test
run: barrnap -q --kingdom arc examples/bacteria.fna
- name: Run test
run: barrnap -q --kingdom mito examples/mitochondria.fna
- name: Run test
run: barrnap -q --kingdom euk examples/fungus.fna
- name: Run test
run: ! barrnap examples/empty.fna
- name: Run test
run: ! barrnap examples/null.fna
- name: Run test
run: barrnap -q examples/small.fna | grep 16S_rRNA
- name: Run test
run: barrnap -q < examples/small.fna | grep 16S_rRNA
- name: Run test
run: barrnap -q - < examples/small.fna | grep 16S_rRNA
- name: Run test
run: barrnap examples/nohits.fna 2>&1 | grep 'Found 0 '
- name: Run test
run: barrnap --threads 2 examples/small.fna
- name: Run test
run: barrnap -q --incseq examples/small.fna | grep '^>'
- name: Run test
run: barrnap -q --outseq hits.fa < examples/small.fna && head -n3 hits.fa
|
