Bootstrap: docker
From: ubuntu:16.04


%environment
    export PATH="$PATH:/opt/MindTheGap/build/ext/gatb-core/bin"

%post
     apt-get -y update && \
     apt-get install -y --no-install-recommends \
     wget \
     gcc \
     g++ \
     make \
     cmake \
     zlib1g-dev \
     libboost-dev \
     bzip2 \
     python2.7 \
     default-jre \
     libbz2-dev \
     liblzma-dev \
     default-jdk \
     python3 \
     python3-pip \
     cython \
     unzip \
     git;\
     git config --global http.sslVerify false;\
     cd /opt;\
     git clone --recursive https://github.com/GATB/MindTheGap.git;\
     cd MindTheGap;\
     git submodule init;\
     git submodule update;\
     mkdir build;\
     cd build;\
     cmake ..;\
     make;\
     cd ..;\
     git config --global http.sslVerify false;\
     pip3 install pyGATB;\
     pip3 install biopython;\
     pip3 install pandas;\
     pip3 install numpy;\


     
     
     
