Dockerfile.apples

# FROM buildpack-deps:precise
FROM ubuntu:12.04
MAINTAINER Bo Gao <bogao@dcs.warwick.ac.uk>

# A. Install OS-level dependencies
RUN apt-get update \
 && apt-get install -y --no-install-recommends \
        build-essential \
        curl \
        procps \
        ncbi-blast+ \
 && rm -rf /var/lib/apt/lists/*

RUN apt-get update \
 && apt-get install -y --no-install-recommends \
        autoconf \
        automake \
        imagemagick \
        libbz2-dev \
        libcurl4-openssl-dev \
        libdb-dev \
        libevent-dev \
        libffi-dev \
        libgeoip-dev \
        libglib2.0-dev \
        libjpeg-dev \
        liblzma-dev \
        libmagickcore-dev \
        libmagickwand-dev \
        libmysqlclient-dev \
        libncurses-dev \
        libpng-dev \
        libpq-dev \
        libreadline-dev \
        libsqlite3-dev \
        libssl-dev \
        libtool \
        libwebp-dev \
        libxml2-dev \
        libxslt-dev \
        libyaml-dev \
        zlib1g-dev \
 && rm -rf /var/lib/apt/lists/*
## Ref: https://github.com/docker-library/buildpack-deps/blob/e7534be05255522954f50542ebf9c5f06485838d/precise/Dockerfile

# B. Install Perl modules
## B1. CPAN modules
RUN cd /usr/src \
    && curl -LO https://raw.githubusercontent.com/miyagawa/cpanminus/master/cpanm \
    && chmod +x cpanm \
    && ./cpanm App::cpanminus \
    && rm -fr ./cpanm /root/.cpanm /usr/src/perl /tmp/*

# RUN curl -L https://cpanmin.us | perl - --sudo App::cpanminus
# RUN cpan App::cpanminus

RUN mkdir /apples
ADD ./cpanfile /apples/cpanfile
RUN cd /apples \
 && cpanm --notest --installdeps .

## B2. Non-CPAN modules (Ensemble API, Ensemblegenomes API and BioPerl)
#       Ref: https://github.com/bogaotory/docker-perl-bio

ENV LIB_NCPAN_PERL /root/lib-perl

RUN mkdir $LIB_NCPAN_PERL

RUN apt-get update \
 && apt-get install -y --no-install-recommends \
        git \
 && rm -rf /var/lib/apt/lists/*

RUN cd $LIB_NCPAN_PERL \
 && git clone https://github.com/Ensembl/ensembl-git-tools.git \
 && echo 'export PATH="'$LIB_NCPAN_PERL'/ensembl-git-tools/bin:$PATH"' >> /root/.profile

RUN . /root/.profile \
 && cd $LIB_NCPAN_PERL \
 && git ensembl --clone api \
 && echo 'export PERL5LIB="'$LIB_NCPAN_PERL'/ensembl/modules:$PERL5LIB"'            >> /root/.profile \
 && echo 'export PERL5LIB="'$LIB_NCPAN_PERL'/ensembl-compara/modules:$PERL5LIB"'    >> /root/.profile \
 && echo 'export PERL5LIB="'$LIB_NCPAN_PERL'/ensembl-funcgen/modules:$PERL5LIB"'    >> /root/.profile \
 && echo 'export PERL5LIB="'$LIB_NCPAN_PERL'/ensembl-io/modules:$PERL5LIB"'     >> /root/.profile \
 && echo 'export PERL5LIB="'$LIB_NCPAN_PERL'/ensembl-variation/modules:$PERL5LIB"'  >> /root/.profile

RUN cd $LIB_NCPAN_PERL \
 && git clone git://github.com/bioperl/bioperl-live.git \
 && git clone https://github.com/bioperl/Bio-EUtilities.git \
 && echo 'export PERL5LIB="'$LIB_NCPAN_PERL'/bioperl-live:$PERL5LIB"'       >> /root/.profile \
 && echo 'export PERL5LIB="'$LIB_NCPAN_PERL'/Bio-EUtilities/lib:$PERL5LIB"' >> /root/.profile

# ENV HOSTNAME=gs
ENV PERL5LIB $LIB_NCPAN_PERL/ensembl/modules:$LIB_NCPAN_PERL/ensembl-compara/modules:$LIB_NCPAN_PERL/ensembl-funcgen/modules:$LIB_NCPAN_PERL/ensembl-io/modules:$LIB_NCPAN_PERL/ensembl-variation/modules:$LIB_NCPAN_PERL/bioperl-live:$LIB_NCPAN_PERL/Bio-EUtilities/lib

# C. Install Conservation module dependencies

RUN apt-get update \
 && apt-get install -y --no-install-recommends \
        wget \
        samtools

RUN cd /tmp \
 && wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz \
 && tar -zxvf bedtools-2.25.0.tar.gz \
 && cd bedtools2 \
 && make \
 && make install

RUN wget https://www.python.org/ftp/python/3.4.5/Python-3.4.5.tar.xz \
 && tar xJf ./Python-3.4.5.tar.xz \
 && cd Python-3.4.5 \
 && ./configure --prefix=/opt/python3.4 \
 && make \
 && make install \
 && ln -s /opt/python3.4/bin/python3.4 /usr/bin/python3.4 \
 && ln -s /opt/python3.4/bin/python3 /usr/bin/python3

RUN  /opt/python3.4/bin/easy_install-3.4 numpy \
 && /opt/python3.4/bin/easy_install-3.4 pandas

# Seaweeds dependencies
RUN apt-get install -y --no-install-recommends \
        libtbb-dev \
        libboost-regex1.48.0 \
        libboost-program-options1.48.0

# D. Patches

# D1.   Install a missing module
#       Since release 1.7.0 Bio::Perl removed Bio::SearchIO::blastxml
#       So we have to install this mobule (required by the rbh module) manually
#       For more info see https://github.com/bioperl/bioperl-live/releases/tag/release-1-7-0
RUN cpanm Bio::SearchIO::blastxml

# Finally

ADD . /apples