Add CI badge #15
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| name: CI | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the "master" branch | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v4 | |
| - uses: shogo82148/actions-setup-perl@v1 | |
| with: | |
| perl-version: "5.38" | |
| - name: Install | |
| run: | | |
| sudo apt-get install -y zip gzip git curl libdb-dev | |
| cpanm --quiet --notest JSON Path::Tiny LWP::Simple Bio::Perl | |
| wget http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.17.0/ncbi-blast-2.17.0+-x64-linux.tar.gz | |
| tar zxvf ncbi-blast-2.17.0+-x64-linux.tar.gz | |
| curl https://raw.githubusercontent.com/tseemann/any2fasta/master/any2fasta > bin/any2fasta | |
| chmod +x bin/any2fasta | |
| export PATH=$PWD/bin:$PWD/ncbi-blast-2.17.0+/bin:$PATH | |
| - name: Test | |
| run: | | |
| export PATH=$PWD/bin:$PWD/ncbi-blast-2.17.0+/bin:$PATH | |
| abricate --setupdb | |
| abricate --version | |
| abricate --help | |
| abricate --check | |
| abricate --list | |
| ! abricate --doesnotexist || echo "fail expected" | |
| ! abricate --threads 0 | |
| ! (abricate test/assembly.fa | grep '~~~') | |
| abricate test/assembly.fa > 1.tab | |
| abricate test/assembly.fa.gz > 2.tab | |
| abricate test/assembly.gbk > 3.tab | |
| abricate test/assembly.gbk.gz > 4.tab | |
| abricate --nopath test/assembly.gbk.gz | grep '^assembly.gbk.gz' | |
| abricate --summary {1,2,3,4}.tab > summary.tab | |
| abricate --summary 1.tab 2.tab 1.tab |& grep 'duplicate' | |
| abricate --summary <(cat 1.tab 2.tab 3.tab) | wc -l | grep -w 4 | |
| abricate test/assembly.txt |& grep ERROR | |
| abricate not_exist.embl |& grep ERROR | |
| abricate --threads `nproc` test/assembly.fa.bz2 | grep -i FOSFOMYCIN | |
| abricate --threads `nproc` test/assembly.fa.bz2 | grep -i lactam | |
| for DB in `abricate --list | cut -f1 | tail -n +2`; do abricate --db $DB test/assembly.fa > /dev/null ; done | |
| abricate-get_db --help | |
| abricate-get_db --db ncbi --dbdir . | |
| ! grep 'FUSIDIC ACID' ncbi/sequences | |
| abricate --threads `nproc` --fofn test/fofn.txt |