anchor.diff:  RUN apt-get install -y mysql-server mysql-client mysql-common bowtie bioperl apache2 libcairo2-dev libpango1.0-dev 
   
   RUN pip3 install biopython==1.68 bcbio-gff==0.6.4 pandas==0.19.1 pybedtools==0.7.8 gffutils regex pysam matplotlib
  +
  +RUN pip pysam matplotlib
   
   WORKDIR /opt/
   
  
positive.code: 
  
  RUN wget https://downloads.sourceforge.net/project/splicegrapher/SpliceGrapher-0.2.5.tgz &&  tar -zxvf SpliceGrapher-0.2.5.tgz && \
      cd SpliceGrapher-0.2.5/ && python3 setup.py build && python3 setup.py install && cd .. \
      && git clone https://bitbucket.org/comp_bio/tapis.git && cd tapis && python3 setup.py build && python3 setup.py install
  
  RUN sudo perl -MCPAN -e shell && sudo cpan -f -i YAML && sudo cpan -f -i Hash::Merge && sudo cpan -f -i  Logger::Simple && sudo cpan -f -i  Parallel::ForkManager &&\
      sudo cpan -f -i Config::Std && sudo cpan -f -i Scalar::Util::Numeric 
  
negative.code: FROM ubuntu:16.04
  
  RUN apt-get clean all && apt-get update && apt-get install -y build-essential apt-utils git wget perl \
      python3.5 python2.7 python3-pip python2.7-pip debconf-utils sudo python-numpy cmake samtools bedtools zlib1g-dev libc6 aptitude \
      libdbd-mysql-perl libdbi-perl libboost-all-dev libncurses5-dev bowtie default-jre parallel nano bowtie2 exonerate
  
  RUN rm /bin/sh && ln -s /bin/bash /bin/sh
  