Dockerfile

FROM centos:6.6

MAINTAINER Vivek Krishnakumar <vivekkrishnakumar@gmail.com>
LABEL version="1.3"

# Set up the base dependencies
RUN yum -q -y update \
  && yum groupinstall -q -y --setopt=group_package_types=optional "Development tools" \
  && yum groupinstall -q -y "Scientific support" \
  && yum install -q -y tar wget git bzip2-devel httpd-devel openssl-devel bind-utils

# Install Python 2.7.9
WORKDIR /tmp
RUN mkdir -p build-markerminer

WORKDIR /tmp/build-markerminer
RUN wget -q https://www.python.org/ftp/python/2.7.9/Python-2.7.9.tgz
RUN tar -zxf Python-2.7.9.tgz

WORKDIR Python-2.7.9
RUN ./configure --prefix=/usr/local --enable-shared LDFLAGS="-Wl,--rpath=/usr/local/lib"
RUN make && make altinstall
WORKDIR /usr/local/bin
RUN ln -sf python2.7 python

# Install setuptools and pip
WORKDIR /tmp/build-markerminer
RUN wget -q https://bootstrap.pypa.io/ez_setup.py -O - | /usr/local/bin/python
RUN wget -q https://bootstrap.pypa.io/get-pip.py -O - | /usr/local/bin/python

# Install required Python modules
RUN pip install --quiet virtualenv
RUN easy_install -f http://biopython.org/DIST/ biopython

# Install NCBI BLAST+
RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-x64-linux.tar.gz
RUN tar -zxf ncbi-blast-2.2.29+-x64-linux.tar.gz
WORKDIR ncbi-blast-2.2.29+/
RUN cp -pr bin/* /usr/local/bin/.

# Install Mafft
WORKDIR /tmp/build-markerminer
RUN wget -q http://mafft.cbrc.jp/alignment/software/mafft-7.215-with-extensions-src.tgz
RUN tar -zxf mafft-7.215-with-extensions-src.tgz
WORKDIR mafft-7.215-with-extensions/core/
RUN make clean && make && make install
WORKDIR ../extensions
RUN make clean && make && make install

# Cleanup temporary build files
WORKDIR /tmp
RUN rm -rf /tmp/build-markerminer

# Set environment for webapp
ENV WWW_DIR /var/www

# Clone the markerminer-webapp repository from bitbucket
RUN mkdir -p $WWW_DIR
WORKDIR $WWW_DIR
RUN git clone --recursive https://github.com/vivekkrish/markerminer-webapp.git markerminer
WORKDIR markerminer
RUN pip install --quiet -r requirements.txt

# Add pipeline executable to PATH
ENV PATH $WWW_DIR/markerminer/pipeline:$PATH

# Set up iptables, expose specific ports (TCP)
EXPOSE 5000

# Start up MarkerMiner web application
CMD python markerminer.py