--- a +++ b/docker/Dockerfile @@ -0,0 +1,48 @@ +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}