Merge pull request #86 from jjmccollum/84-add-option-for-choice-of-an… #207
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name: beast | |
on: [push] | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.10"] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Install Java 17 | |
uses: actions/setup-java@v3 | |
with: | |
java-package: 'jdk+fx' | |
distribution: 'zulu' | |
java-version: '17.0.6+10' | |
- name: Install poetry | |
run: pipx install poetry | |
- name: Install dependencies for Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v3 | |
with: | |
python-version: ${{ matrix.python-version }} | |
cache: 'poetry' | |
- run: poetry install | |
- name: Testing | |
run: | | |
poetry run teiphy -t reconstructed -t defective -t orthographic -t subreading -m overlap -m lac -s"*" -s T --fill-correctors --clock strict --seed 1337 example/ubs_ephesians.xml beast_strict_example.xml | |
poetry run teiphy -t reconstructed -t defective -t orthographic -t subreading -m overlap -m lac -s"*" -s T --fill-correctors --clock uncorrelated --seed 1337 example/ubs_ephesians.xml beast_uncorrelated_example.xml | |
poetry run teiphy -t reconstructed -t defective -t orthographic -t subreading -m overlap -m lac -s"*" -s T --fill-correctors --clock local --seed 1337 example/ubs_ephesians.xml beast_local_example.xml | |
- name: Install Phylogenetics Package | |
run: | | |
export JAVA_HOME=/opt/hostedtoolcache/Java_Zulu_jdk+fx/17.0.6-10/x64 | |
export PATH=${JAVA_HOME}/bin:${PATH} | |
git clone https://github.com/CompEvol/beast2.git | |
git clone https://github.com/CompEvol/BeastFX.git | |
cd BeastFX | |
ant -DopenjreLnx=$JAVA_HOME linux | |
cd ~ | |
mkdir .beast | |
cd .beast | |
cp /home/runner/work/teiphy/teiphy/beast2/release/Linux/*.tgz . | |
tar zxvf *.tgz | |
~/.beast/beast/bin/packagemanager -add BEAST_CLASSIC | |
~/.beast/beast/bin/packagemanager -add BEASTLabs | |
~/.beast/beast/bin/packagemanager -add BDSKY | |
- name: Phylogenetics Run | |
run: | | |
~/.beast/beast/bin/beast -overwrite beast_strict_example.xml | |
~/.beast/beast/bin/beast -overwrite beast_uncorrelated_example.xml | |
~/.beast/beast/bin/beast -overwrite beast_local_example.xml | |