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Dockerfile to build pylibseq
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FROM opensciencegrid/osgvo-ubuntu-18.04:latest | |
#maintainer "Ariella Gladstein <aglad@med.unc.edu>" | |
#organization "University of North Carolina at Chapel Hill" | |
#department "Genetics" | |
#date "30 Auguest 2019" | |
#application "pylibseq, for calculating population genetic statistics on genotype data" | |
RUN apt-get update && apt-get install -y --no-install-recommends \ | |
build-essential \ | |
cmake \ | |
git \ | |
libgsl0-dev \ | |
python3 \ | |
python3-dev \ | |
python3-pip \ | |
python3.6-venv \ | |
ipython3 \ | |
python3-numpy \ | |
sqlite3 \ | |
vim \ | |
curl \ | |
&& \ | |
apt-get clean && \ | |
rm -rf /var/lib/apt/lists/* | |
RUN git clone --depth 1 https://github.com/molpopgen/pylibseq.git \ | |
&& cd pylibseq \ | |
&& git submodule update --init --recursive \ | |
&& git submodule status --recursive | |
WORKDIR /pylibseq | |
RUN pip3 install setuptools wheel | |
RUN pip3 install --user -r requirements.txt | |
RUN pip3 install --user cppimport twine msprime | |
WORKDIR / | |
RUN curl -L https://github.com/pybind/pybind11/archive/v2.2.4.tar.gz > pybind11-2.2.4.tar.gz \ | |
&& tar xzf pybind11-2.2.4.tar.gz | |
WORKDIR /pybind11-2.2.4 | |
RUN cmake . -DPYBIND11_PYTHON_VERSION=3.6.8 -DPYBIND11_TEST=0 \ | |
&& make install | |
ENV PATH="/root/.local/bin:${PATH}" | |
WORKDIR /pylibseq | |
RUN python3 setup.py build_ext --inplace | |
#RUN python3 -m unittest discover tests | |
RUN python3 setup.py sdist \ | |
&& python3 setup.py check \ | |
&& python3 -m twine check dist/*.tar.gz | |
RUN python3 -m venv venv \ | |
&& ./venv/bin/pip3 install --upgrade setuptools pip pybind11 \ | |
&& ./venv/bin/pip3 install dist/pylibseq-0.2.3.tar.gz | |
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