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FROM discoenv/jupyter-lab:beta
USER root
# Update the packages
RUN apt-get update \
&& apt-get clean \
&& rm -rf /usr/lib/apt/lists/*
USER jovyan
# Install ipykernel & Biopython
RUN python3 -m pip install ipykernel \
&& pip install biopython==1.72
# Install OpenJDK & PySpark
RUN conda install openjdk==8.0.152 pyspark==2.4.3 -y
# Install mmtfPySpark
RUN pip install git+https://github.com/sbl-sdsc/mmtf-pyspark.git
WORKDIR /home/jovyan
# Set default environment variables for MMTF Hadoop Sequence files
ARG MMTF_FULL_ENV=/home/jovyan/full
ENV MMTF_FULL=$MMTF_FULL_ENV
ARG MMTF_REDUCED_ENV=/home/jovyan/reduced
ENV MMTF_REDUCED=$MMTF_REDUCED_ENV
# Set default environment variables for PySpark
ARG MASTER_ENV=local[4]
ENV MASTER=$MASTER_ENV
# Disable multi-threading of Intel MKL and OpenBLAS
ENV OPENBLAS_NUM_THREADS=1
ENV MKL_NUM_THREADS=1
ENV OMP_NUM_THREADS=1
# Clone mmtf-genomics
RUN git clone https://github.com/sbl-sdsc/mmtf-genomics
COPY entry.sh /bin
RUN mkdir /home/jovyan/.irods
ENTRYPOINT ["/bin/entry.sh"]
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