# Ubuntu base image 
FROM ubuntu:14.04
MAINTAINER Benjamin Schubert <schubert@infomratik.uni-tuebingen.de>

#installation of software
RUN apt-get update && apt-get install -y software-properties-common \
&& apt-get install -y python-software-properties \
&& add-apt-repository ppa:git-core/ppa \
&& add-apt-repository ppa:george-edison55/cmake-3.x \
&& add-apt-repository ppa:ubuntu-toolchain-r/test \
&& apt-get update && apt-get install -y \
    gcc-4.9 \
    g++-4.9 \
    build-essential \
    coinor-cbc \
    git \
    mercurial \
    curl \
    libcurl4-openssl-dev \
    pkg-config \
    python \
    python-pip \
    python-dev \
    cython \
    libfreetype6-dev \
    libmysqlclient-dev \
    libboost-dev \
    libboost-serialization-dev \
    zlib1g-dev \
    tcsh \
    gawk \
    cmake \
    r-base \
    bowtie \
    libbz2-dev \
    liblzma-dev \
    liblzo2-dev \
&& update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9 \
&& rm -rf /var/lib/apt/lists/* \
&& apt-get clean \
&& apt-get purge


RUN git clone https://github.com/FRED-2/ImmunoNodes.git \
    && make -C /ImmunoNodes/src \
    && chmod -R 777 /ImmunoNodes/

#get contribs
RUN  mkdir /usr/src/LKH \
    && mkdir /usr/src/hdf5 \
    && mkdir -p /ImmunoNodes/src/data/tries \
    && curl -Lo /ImmunoNodes/src/data/tries/uniprot_proteome_l8.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l8.trie" \
    && curl -Lo /ImmunoNodes/src/data/tries/uniprot_proteome_l9.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l9.trie" \
    && curl -Lo /ImmunoNodes/src/data/tries/uniprot_proteome_l10.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l10.trie" \
    && curl -Lo /ImmunoNodes/src/data/tries/uniprot_proteome_l11.trie "https://netcologne.dl.sourceforge.net/project/immunonode-files/uniprot_proteome_l11.trie" \
    && curl -Lo /usr/local/pkg_predictors.tar.gz  "https://netcologne.dl.sourceforge.net/project/immunonode-files/contrib/pkg_predictors.tar.gz" \
    && curl -Lo /usr/src/LKH/LKH-2.0.7.tgz  "https://netcologne.dl.sourceforge.net/project/immunonode-files/contrib/LKH-2.0.7.tgz" \
    && curl -Lo /usr/src/hdf5/hdf5.tar.gz  "https://netcologne.dl.sourceforge.net/project/immunonode-files/contrib/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared.tar.gz" \
    && tar -xzf /usr/local/pkg_predictors.tar.gz  -C /usr/local/ \
    && tar -xzf /usr/src/LKH/LKH-2.0.7.tgz -C /usr/src/LKH/ \
    && tar -xvf /usr/src/hdf5/hdf5.tar.gz -C /usr/src/hdf5/ \
    && mv /usr/src/hdf5/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/bin/* /usr/local/bin/ \
    && mv /usr/src/hdf5/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/lib/* /usr/local/lib/ \
    && mv /usr/src/hdf5/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/include/* /usr/local/include/ \
    && mv /usr/src/hdf5/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared/share/* /usr/local/share/ \
    && make -C /usr/src/LKH/LKH-2.0.7/ \
    && mv /usr/src/LKH/LKH-2.0.7/LKH /usr/local/bin/ \
    && rm -rf /usr/src/LKH/ \
    && rm -f /usr/local/pkg_predictors.tar.gz \
    && rm -rf /usr/src/hdf5/



#HLA Typing
#OptiType dependecies


ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH
ENV HDF5_DIR /usr/local/

RUN pip install --upgrade pip && pip install \
    setuptools==33.1.1 \
    tornado==4.5.3 \
    numpy==1.14.5 \
    pyomo==4.4.1 \
    pysam==0.14.1 \
    tables==3.4.4 \
    pandas==0.23.2 \
    future==0.16.0 \
    matplotlib==1.4.3 \
    && pip install git+https://github.com/FRED-2/Fred2@master

#installing optitype form git repository (version Dec 09 2015) and wirtig config.ini
RUN git clone https://github.com/FRED-2/OptiType.git \
    && sed -i -e '1i#!/usr/bin/env python\' OptiType/OptiTypePipeline.py \
    && mv OptiType/ /usr/local/bin/ \
    && chmod 777 /usr/local/bin/OptiType/OptiTypePipeline.py \
    && echo "[mapping]\n\
razers3=/usr/local/bin/razers3 \n\
threads=1 \n\
\n\
[ilp]\n\
solver=cbc \n\
threads=1 \n\
\n\
[behavior]\n\
deletebam=true \n\
unpaired_weight=0 \n\
use_discordant=false\n" >> /usr/local/bin/OptiType/config.ini


#installing razers3
RUN git clone https://github.com/seqan/seqan.git seqan-src \
    && cd seqan-src \
    && cmake -DCMAKE_BUILD_TYPE=Release \
    && make razers3 \
    && cp bin/razers3 /usr/local/bin \
    && cd .. \
    && rm -rf seqan-src

#Seq2HLA
RUN hg clone https://bitbucket.org/sebastian_boegel/seq2hla \
    && sed -i -e '1i#!/usr/bin/env python\' seq2hla/seq2HLA.py \
    && mv seq2hla/ /usr/local/bin/ \
    && chmod 777 /usr/local/bin/seq2hla/seq2HLA.py 

#Fred2
#RUN pip install --upgrade pip && pip install git+https://github.com/FRED-2/Fred2@master


#set envirnomental variables for prediction methods
ENV NETCHOP /usr/local/predictors/netchop/netchop-3.1
ENV TMPDIR /tmp
ENV PATH /ImmunoNodes/src/:/usr/local/bin/OptiType:/usr/local/bin/seq2hla:/usr/local/predictors/bin:$PATH