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try manually installing syri dependencies from pypi
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lrauschning committed Dec 10, 2024
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4 changes: 3 additions & 1 deletion .github/workflows/build.yml
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Expand Up @@ -30,7 +30,9 @@ jobs:
python -m pip install --upgrade pip setuptools
# apparently the runners all have conda installed
# use that to install syri, as it isn't on pypi
$CONDA/bin/conda install -c conda-forge -c bioconda "syri>=1.6.5"
# manually install syris dependencies, conda does not install
pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp
$CONDA/bin/conda install --freeze-installed --no-deps -c conda-forge -c bioconda "syri>=1.6.5"
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Build package
run: pip install .
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