Updated Readme and Changelog. #746
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name: chewbbaca | |
on: | |
push: | |
branches: [ master ] | |
pull_request: | |
branches: [ master ] | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.8', '3.9', '3.10', '3.11'] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install pytest | |
pip install pytest-forked | |
pip install py | |
- name: install blast | |
run: | | |
mkdir $GITHUB_WORKSPACE/blast | |
pushd $GITHUB_WORKSPACE/blast | |
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz \ | |
&& tar -xzvf ncbi-blast-2.9.0+-x64-linux.tar.gz && rm ncbi-blast-2.9.0+-x64-linux.tar.gz | |
echo "$GITHUB_WORKSPACE/blast/ncbi-blast-2.9.0+/bin" >> $GITHUB_PATH | |
popd | |
- name: check blast | |
run: | | |
which blastp | |
blastp -version | |
- name: install mafft | |
run: | | |
mkdir $GITHUB_WORKSPACE/mafft | |
pushd $GITHUB_WORKSPACE/mafft | |
wget https://mafft.cbrc.jp/alignment/software/mafft_7.475-1_amd64.deb | |
sudo dpkg -i mafft_7.475-1_amd64.deb | |
popd | |
- name: check mafft | |
run: | | |
which mafft | |
mafft --version | |
- name: install fasttree2 | |
run: | | |
mkdir $GITHUB_WORKSPACE/fasttree2 | |
pushd $GITHUB_WORKSPACE/fasttree2 | |
wget https://anaconda.org/bioconda/fasttree/2.1.11/download/linux-64/fasttree-2.1.11-h031d066_2.tar.bz2 | |
bzip2 -d fasttree-2.1.11-h031d066_2.tar.bz2 && tar -xvf fasttree-2.1.11-h031d066_2.tar && rm fasttree-2.1.11-h031d066_2.tar | |
echo "$GITHUB_WORKSPACE/fasttree2/bin" >> $GITHUB_PATH | |
popd | |
- name: check fasttree2 | |
run: | | |
which FastTree | |
FastTree -help | |
- name: checkout chewbbaca | |
uses: actions/checkout@v4 | |
with: | |
repository: B-UMMI/chewBBACA | |
path: chewbbaca | |
- name: install chewbbaca | |
run: | | |
pushd $GITHUB_WORKSPACE/chewbbaca | |
python -m pip install . | |
- name: check chewbbaca | |
run: | | |
which chewBBACA.py | |
- name: run pytest | |
run: | | |
pushd CHEWBBACA/tests | |
pytest --forked | |
popd |