update pipeline for new dfe with h-s relationship #152
Workflow file for this run
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| name: dry-run | |
| on: ['push', 'pull_request'] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.10" | |
| - name: Add micromamba to system path | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-name: analysis2 | |
| activate-environment: analysis2 | |
| environment-file: environment.yml | |
| - name: Install DFE-alpha | |
| run: | | |
| cd ext | |
| wget -c https://sourceforge.net/projects/dfe-alpha-k-e-w/files/dfe-alpha-release-2.16.tar.gz/download | |
| mv download dfe-alpha-release-2.16.tar.gz | |
| tar -xvf dfe-alpha-release-2.16.tar.gz | |
| cat dfe_alpha_makefile_stdpopsim_patch > dfe-alpha-release-2.16/Makefile | |
| cd dfe-alpha-release-2.16 | |
| micromamba run -n analysis2 make | |
| cd ../../ | |
| - name: Install msmc | |
| run: | | |
| cd ext | |
| git clone https://github.com/stschiff/msmc2.git | |
| cat msmc2_makefile_stdpopsim_patch > msmc2/Makefile | |
| cd msmc2 | |
| micromamba run -n analysis2 make | |
| cd ../../ | |
| - name: Install smc++ | |
| run: | | |
| cd ext | |
| git clone https://github.com/popgenmethods/smcpp | |
| cat smc_setup_stdpopsim_patch > smcpp/setup.py | |
| cat smc_pyproject_stdpopsim_patch > smcpp/pyproject.toml | |
| cd smcpp | |
| micromamba run -n analysis2 pip install . | |
| cd ../../ | |
| - name: Test dry-run | |
| run: | | |
| micromamba run -n analysis2 snakemake -np --use-conda --conda-frontend conda |