anchor.diff:  #
   # VERSION       0.1
   # This Dockerfile is the base system for executing scripts by the DockerToolFactory.
  -
   FROM debian:jessie
  -
  -MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com
  -
  +#original ... MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com
  +MAINTAINER Michael T Lovci michaeltlovci@gmail.com
   # make sure the package repository is up to date
   ENV DEBIAN_FRONTEND noninteractive
   RUN apt-get -qq update
  -
   # Install all requirements that are recommend by the Galaxy project
   RUN apt-get install --no-install-recommends -y autoconf automake build-essential gfortran \
   cmake git-core libatlas-base-dev libblas-dev liblapack-dev mercurial subversion python-dev \
   pkg-config openjdk-7-jre python-setuptools adduser zlib1g-dev ghostscript r-base-core \
    graphicsmagick-imagemagick-compat
  -
   RUN apt-get install -y python-virtualenv libfreetype6-dev exonerate bedtools wget curl \
   libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev samtools liblzma-dev \
   libpcre3-dev libbz2-dev
  -
   RUN easy_install pip
  -
   RUN pip install --upgrade numpy pysam tornado matplotlib pip pandas ipython rpy2 
   RUN pip install scikit-learn 
   RUN pip install cython 
   RUN pip install setuptools 
  -
   RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("DESeq", "DESeq2", "edgeR", "EDASeq"))'
   RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")'
   RUN apt-get install bc
  
positive.code: RUN wget http://weblogo.berkeley.edu/release/weblogo.2.8.2.tar.gz -O weblogo.2.8.2.tar.gz && tar zxvf weblogo.2.8.2.tar.gz && cp weblogo/seqlogo /usr/bin/.
  RUN wget http://homer.salk.edu/homer/configureHomer.pl -O configureHomer.pl && perl configureHomer.pl -install homer
  RUN adduser galaxy -u 451
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  RUN pip install --upgrade git+https://github.com/matplotlib/matplotlib.git
  
  RUN apt-get update
  RUN apt-get install -y emacs
  
  RUN apt-get install -y emboss emboss-lib
  #RUN wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz && tar xzvf EMBOSS-6.6.0.tar.gz && cd EMBOSS-6.6.0 && ./configure --without-x &&  make && make install
  RUN apt-get install -y mysql-client
  
negative.code: ADD install_bionode.sh /install_bionode.sh
  RUN bash /install_bionode.sh
  ENV PATH /weblogo:$PATH
  RUN usermod -aG staff galaxy
  #VOLUME ["/home/galaxy/"]
  RUN mkdir /home/galaxy/job_working_directory
  WORKDIR /home/galaxy/job_working_directory
  USER galaxy
  #ENTRYPOINT chown -R galaxy /home/galaxy/ && su - galaxy
  CMD /bin/bash
  