FROM ubuntu:16.04

ENV NEUSOMATIC_VERSION 0.2.1

ENV ZLIB_VERSION 1.2.11

ENV NUMPY_VERSION 1.15.4

ENV SCIPY_VERSION 1.2.0

ENV IMAGEIO_VERSION 2.5.0

ENV PYTORCH_VERSION 1.1.0

ENV TORCHVISION_VERSION 0.3.0

ENV CUDATOOLKIT_VERSION 9.0

ENV CMAKE_VERSION 3.13.2

ENV PYBEDTOOLS_VERSION 0.8.0

ENV PYSAM_VERSION 0.15.2

ENV SAMTOOLS_VERSION 1.9

ENV TABIX_VERSION 0.2.6

ENV BEDTOOLS_VERSION 2.27.1

ENV BIOPYTHON_VERSION 1.72

ENV GCC_VERSION 5

RUN apt-get update && apt-get install -y --fix-missing \

                build-essential zlib1g-dev curl less vim bzip2

RUN apt-get install -y --fix-missing git wget

RUN curl -LO http://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}

ENV LD_LIBRARY_PATH=/miniconda/lib:${LD_LIBRARY_PATH}

RUN conda update -y conda

RUN conda install -y zlib=${ZLIB_VERSION} numpy=${NUMPY_VERSION} scipy=${SCIPY_VERSION} \

                     imageio=${IMAGEIO_VERSION} && conda clean -a

RUN conda install -y cmake=${CMAKE_VERSION} -c conda-forge && conda clean -a

RUN conda install -y pysam=${PYSAM_VERSION} pybedtools=${PYBEDTOOLS_VERSION} \

                     samtools=${SAMTOOLS_VERSION} tabix=${TABIX_VERSION} \

                     bedtools=${BEDTOOLS_VERSION} \

                     biopython=${BIOPYTHON_VERSION} -c bioconda && conda clean -a

RUN conda install -y pytorch=${PYTORCH_VERSION} \

                     torchvision=${TORCHVISION_VERSION} \

                     cudatoolkit=${CUDATOOLKIT_VERSION} -c pytorch && conda clean -a

RUN apt-get install -y --fix-missing gcc-${GCC_VERSION} g++-${GCC_VERSION}

ADD https://github.com/bioinform/neusomatic/archive/v${NEUSOMATIC_VERSION}.tar.gz /opt/v${NEUSOMATIC_VERSION}.tar.gz 

RUN cd /opt/ && tar -xzvf v${NEUSOMATIC_VERSION}.tar.gz && mv neusomatic-${NEUSOMATIC_VERSION} neusomatic && rm /opt/v${NEUSOMATIC_VERSION}.tar.gz

RUN cd /opt/neusomatic/ && ./build.sh 

ENV PATH=/opt/neusomatic/neusomatic/bin:/opt/neusomatic/neusomatic/python/:${PATH}