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Updated Readme and Changelog. #746

Updated Readme and Changelog.

Updated Readme and Changelog. #746

Workflow file for this run

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