Dockerfile

FROM ubuntu:16.04
MAINTAINER Yuichi Shiraishi <friend1ws@gmail.com> 


RUN apt-get update && apt-get install -y \
    git \
    wget \
    bzip2 \
    make \
    gcc \
    zlib1g-dev \
    libbz2-dev \
    liblzma-dev \
    libcurl4-openssl-dev \
    libssl-dev \
    python \
    python-pip \
    bwa

RUN wget https://github.com/samtools/htslib/releases/download/1.7/htslib-1.7.tar.bz2 && \
    tar jxvf htslib-1.7.tar.bz2 && \
    cd htslib-1.7 && \
    ./configure && \
    make && \
    make install

RUN pip install 'pip>=20,<21'
RUN pip install 'setuptools>=44,<45'

RUN pip install annot_utils==0.2.1
RUN pip install pysam==0.15
RUN pip install numpy==1.15.1
RUN pip install scipy==1.1.0
RUN pip install edlib

COPY . /root/GenomonSV
RUN cd /root/GenomonSV && python setup.py install

# for blat
RUN apt-get update && apt-get install -y \
    libkrb5-3 \
    libpng12-0

# sv_utils
RUN pip install sv_utils==0.5.1
RUN pip install primer3-py==0.5.5