FROM debian:jessie-backports

#----------------------------
# Install debian dependencies
#----------------------------
RUN apt-get update &&  \
    apt-get -t jessie-backports install -y --no-install-recommends \
    ca-certificates \
    g++ \
    less \
    libdbd-mysql-perl \
    libdbi-perl \
    make \
    mysql-client \
    perl \
    tar \
    wget \
    && apt-get clean && \
    rm -rf /var/lib/apt/lists/*

# Make a software folder
RUN mkdir /software

#--------------
# Install blast
#--------------
RUN cd /software \
    && wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/blast-2.2.26-x64-linux.tar.gz \
    && tar -xzvf blast-2.2.26-x64-linux.tar.gz \
    && rm blast-2.2.26-x64-linux.tar.gz

#--------------
# Install MCL
#--------------
RUN cd /software \
    && wget http://micans.org/mcl/src/mcl-14-137.tar.gz \
    && tar -xzvf mcl-14-137.tar.gz \
    && rm mcl-14-137.tar.gz \
    && cd /software/mcl-14-137 \
    && ./configure --enable-blast --prefix=/software/mcl \
    && make install \
    && cd /software \
    && rm -rf /software/mcl-14-137

#-----------------
# Install OrthoMCL
#-----------------
RUN cd /software \
    && wget http://www.orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz \
    && tar -xzvf orthomclSoftware-v2.0.9.tar.gz \
    && rm orthomclSoftware-v2.0.9.tar.gz

#----------------
# Setup the paths
#----------------
ENV PATH $PATH:/software/blast-2.2.26/bin
ENV PATH $PATH:/software/mcl/bin
ENV PATH $PATH:/software/orthomclSoftware-v2.0.9/bin

#------------------
# Add config script
#------------------
ADD test_run/create_config.sh /software/create_config.sh