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Dockerfile
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# Python support can be specified down to the minor or micro version
# (e.g. 3.6 or 3.6.3).
# OS Support also exists for jessie & stretch (slim and full).
# See https://hub.docker.com/r/library/python/ for all supported Python
# tags from Docker Hub.
FROM ubuntu:16.04
LABEL Name=hicstuff Version=2.3.0
# Install python dependencies
COPY * ./ /app/
WORKDIR /app
# System packages
RUN apt-get update && apt-get install -y curl
# Install miniconda to /miniconda
RUN curl -LO https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
RUN bash Miniconda3-latest-Linux-x86_64.sh -p /miniconda -b
RUN rm Miniconda3-latest-Linux-x86_64.sh
ENV PATH=/miniconda/bin:${PATH}
RUN conda update -y conda
RUN conda config --add channels bioconda
# Get 3rd party packages directly from conda
RUN conda install -c conda-forge -y \
bowtie2 \
minimap2 \
bwa \
samtools \
htslib \
pysam \
cooler
RUN pip install -Ur requirements.txt
# Using pip:
RUN pip install .
#CMD ["python3", "-m", "hicstuff.main"]
ENTRYPOINT [ "hicstuff" ]