anchor.diff:  ADD install_bionode.sh /install_bionode.sh
   RUN bash /install_bionode.sh
   ENV PATH /weblogo:$PATH
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   RUN usermod -aG staff galaxy
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   #VOLUME ["/home/galaxy/"]
   RUN mkdir /home/galaxy/job_working_directory
   WORKDIR /home/galaxy/job_working_directory
   USER galaxy
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   #ENTRYPOINT chown -R galaxy /home/galaxy/ && su - galaxy
   CMD /bin/bash
  
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: #
  # VERSION       0.1
  # This Dockerfile is the base system for executing scripts by the DockerToolFactory.
  FROM debian:jessie
  #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
  