Dockerfile

FROM ubuntu:xenial
LABEL maintainer "sujaikumar@gmail.com"

RUN apt-get update && apt-get upgrade -y -q

RUN apt-get install -y -q \
    software-properties-common \
    libboost-iostreams-dev libboost-system-dev libboost-filesystem-dev \
    zlibc gcc-multilib apt-utils zlib1g-dev python \
    cmake tcsh build-essential g++ git wget gzip perl cpanminus

COPY gm_et_linux_64.tar.gz /

RUN tar -xzf gm_et_linux_64.tar.gz

RUN wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz

RUN tar -xzf augustus-3.2.3.tar.gz

RUN apt-get install bamtools -y -q

RUN wget http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1_v1.10.tar.gz 2>/dev/null

RUN tar -xzf BRAKER1_v1.10.tar.gz

RUN apt-get install samtools -y -q

RUN cpanm File::Spec::Functions Hash::Merge List::Util Logger::Simple \
      Module::Load::Conditional Parallel::ForkManager POSIX Scalar::Util::Numeric YAML

RUN adduser --disabled-password --gecos '' dockeruser
RUN mkdir /data
RUN chown -R dockeruser /data
RUN chmod a+w -R /augustus-3.2.3/config
USER dockeruser
WORKDIR /data

COPY gm_key_64.gz ~/
RUN zcat ~/gm_key_64.gz > ~/.gm_key

ENV PATH $PATH:/BRAKER1_v1.10:/augustus-3.2.3/bin/
ENV PATH $PATH:/augustus-3.2.3/scripts:/gm_et_linux_64/gmes_petap/
ENV AUGUSTUS_CONFIG_PATH /augustus-3.2.3/config
ENV GENEMARK_PATH /gm_et_linux_64/gmes_petap/
ENV BAMTOOLS_PATH /usr/bin/