agladstein/pylibseq repository overview

FROM opensciencegrid/osgvo-ubuntu-18.04:latest

#maintainer "Ariella Gladstein <[email protected]>"
#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 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