Dockerfile

FROM bioperl/bioperl:release-1-7-1

LABEL maintainer "erik.kastman@gmail.com"

ENV DEBIAN_FRONTEND noninteractive

# Versions for ubuntu:14.04 (bioperl, trusty)
RUN echo 'deb http://us.archive.ubuntu.com/ubuntu trusty multiverse' >> /etc/apt/sources.list

# Add Additional System Utils
RUN apt-get update && \
    apt-get install -y \
      patch \
      wget

RUN apt-get install -y \
      mafft=7.123-1 \
      mcl=1:12-135-2 \
      openjdk-7-jre-headless \
      phylip=1:3.695-1 && \
    apt-get clean

ARG pgap_version=1.2.1

COPY PGAP-${pgap_version}.md5 /PGAP-${pgap_version}.md5
RUN wget https://downloads.sourceforge.net/project/pgap/PGAP-${pgap_version}/PGAP-${pgap_version}.tar.gz && \
  md5sum -c PGAP-${pgap_version}.md5 && \
  tar xzf PGAP-${pgap_version}.tar.gz && \
  mv /PGAP-${pgap_version} /pgap && \
  chmod a+x /pgap/*.pl && \
  rm PGAP-${pgap_version}.tar.gz

COPY updatePaths.patch /updatePaths.patch
RUN patch /pgap/PGAP.pl < /updatePaths.patch
RUN rm /updatePaths.patch

RUN (echo y;echo o conf prerequisites_policy follow;echo o conf commit)|cpan && \
    cpan Statistics::LineFit && \
    cpan Statistics::Distributions;

WORKDIR /pgap
ENTRYPOINT ["/pgap/PGAP.pl"]
CMD ["-h"]