anchor.diff:      chmod a+rwx /usr/local/share/bcbio-nextgen && \
       chmod a+rwx /usr/local/share/bcbio-nextgen/config && \
       chmod a+rwx /usr/local/share/bcbio-nextgen/config/*.yaml && \
  -    chmod a+rwx /usr/local/share/bcbio-nextgen/gemini-config.yaml
  +    chmod a+rwx /usr/local/share/bcbio-nextgen/gemini-config.yaml && \
   
   # Ensure permissions are set for update in place by arbitrary users
  -RUN find /usr/local -perm /u+x -execdir chmod a+x {} \;
  -RUN find /usr/local -perm /u+w -execdir chmod a+w {} \;+    find /usr/local -perm /u+x -execdir chmod a+x {} \; && \
  +    find /usr/local -perm /u+w -execdir chmod a+w {} \;
  
positive.code: FROM stackbrew/ubuntu:14.04
  MAINTAINER Brad Chapman "https://github.com/chapmanb"
  
  # Setup a base system 
  RUN apt-get update && apt-get install -y build-essential zlib1g-dev wget curl python-setuptools git
  RUN apt-get install -y openjdk-7-jdk openjdk-7-jre ruby libncurses5-dev libcurl4-openssl-dev libbz2-dev \
      unzip pigz bsdmainutils
  
  # Fake a fuse install; openjdk pulls this in 
  # https://github.com/dotcloud/docker/issues/514
  # https://gist.github.com/henrik-muehe/6155333
  RUN mkdir -p /tmp/fuse-hack && cd /tmp/fuse-hack && \
      apt-get install libfuse2 && \
      apt-get download fuse && \
      dpkg-deb -x fuse_* . && \
  
negative.code:     rm -rf $(brew --cache) && \
      rm -rf /usr/local/.git && \
      rm -rf /.cpanm && \
      rm -rf /tmp/bcbio-nextgen-install && \
  
  # Create directories and symlinks for data 
      mkdir -p /mnt/biodata && \
      mkdir -p /tmp/bcbio-nextgen && \
      mv /usr/local/share/bcbio-nextgen/galaxy/bcbio_system.yaml /usr/local/share/bcbio-nextgen/config && \
      rmdir /usr/local/share/bcbio-nextgen/galaxy && \
  