anchor.diff:  
   # specifies files to include as data libraries
   ADD setup_data_libraries.py /galaxy-central/
  -ADD setup_data_libraries.ini /galaxy-central/
   
   ENV GALAXY_CONFIG_JOB_WORKING_DIRECTORY=/galaxy-central/database/job_working_directory \
  -GALAXY_CONFIG_FILE_PATH=/galaxy-central/database/files \
  -GALAXY_CONFIG_NEW_FILE_PATH=/galaxy-central/database/files \
  -GALAXY_CONFIG_TEMPLATE_CACHE_PATH=/galaxy-central/database/compiled_templates \
  -GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=/galaxy-central/database/citations/data \
  -GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=/galaxy-central/database/pbs \
  -GALAXY_CONFIG_FTP_UPLOAD_DIR=/galaxy-central/database/ftp \
  -GALAXY_CONFIG_INTEGRATED_TOOL_PANEL_CONFIG=/galaxy-central/integrated_tool_panel.xml \
  -GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True
  +    GALAXY_CONFIG_FILE_PATH=/galaxy-central/database/files \
  +    GALAXY_CONFIG_NEW_FILE_PATH=/galaxy-central/database/files \
  +    GALAXY_CONFIG_TEMPLATE_CACHE_PATH=/galaxy-central/database/compiled_templates \
  +    GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=/galaxy-central/database/citations/data \
  +    GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=/galaxy-central/database/pbs \
  +    GALAXY_CONFIG_FTP_UPLOAD_DIR=/galaxy-central/database/ftp \
  +    GALAXY_CONFIG_INTEGRATED_TOOL_PANEL_CONFIG=/galaxy-central/integrated_tool_panel.xml \
  +    GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True
   
  -RUN start_galaxy_for_build && . $GALAXY_VIRTUALENV/bin/activate && python -u setup_data_libraries.py && supervisorctl stop all
  +RUN start_galaxy_for_build && . $GALAXY_VIRTUALENV/bin/activate && python -u setup_data_libraries.py --verbose && supervisorctl stop all
   
   ENV GALAXY_CONFIG_JOB_WORKING_DIRECTORY=/export/galaxy-central/database/job_working_directory \
  -GALAXY_CONFIG_FILE_PATH=/export/galaxy-central/database/files \
  -GALAXY_CONFIG_NEW_FILE_PATH=/export/galaxy-central/database/files \
  -GALAXY_CONFIG_TEMPLATE_CACHE_PATH=/export/galaxy-central/database/compiled_templates \
  -GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=/export/galaxy-central/database/citations/data \
  -GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=/export/galaxy-central/database/pbs \
  -GALAXY_CONFIG_FTP_UPLOAD_DIR=/export/galaxy-central/database/ftp \
  -GALAXY_CONFIG_INTEGRATED_TOOL_PANEL_CONFIG=/galaxy-central/integrated_tool_panel.xml
  +    GALAXY_CONFIG_FILE_PATH=/export/galaxy-central/database/files \
  +    GALAXY_CONFIG_NEW_FILE_PATH=/export/galaxy-central/database/files \
  +    GALAXY_CONFIG_TEMPLATE_CACHE_PATH=/export/galaxy-central/database/compiled_templates \
  +    GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=/export/galaxy-central/database/citations/data \
  +    GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=/export/galaxy-central/database/pbs \
  +    GALAXY_CONFIG_FTP_UPLOAD_DIR=/export/galaxy-central/database/ftp \
  +    GALAXY_CONFIG_INTEGRATED_TOOL_PANEL_CONFIG=/export/galaxy-central/integrated_tool_panel.xml
   
  -# Mark folders as imported from the host.
  -VOLUME ["/export/", "/data/", "/var/lib/docker"]
  -
  -# Autostart script that is invoked during container start
  -CMD ["/usr/bin/startup"]
  +# Volumnes and CMD are defined by the parent container
  +#VOLUME ["/export/", "/data/", "/var/lib/docker"]
  +#CMD ["/usr/bin/startup"]
  
positive.code:     "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_randfold_2_0 " \
      "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mirdeep2_mapper --panel-section-name RNATools" \
      "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mirdeep2_quantifier --panel-section-name RNATools" \
      "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mirdeep2 --panel-section-name RNATools"
  
  RUN install-repository     "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name suite_mirdeep_2_0"
  
  RUN curl -sL https://github.com/bgruening/galaxytools/archive/master.tar.gz > master.tar.gz && tar -xf master.tar.gz galaxytools-master/visualisations
  RUN cp -r galaxytools-master/visualisations/* config/plugins/visualizations/
  RUN rm master.tar.gz
  
  # need bioblend for api/install triggers
  RUN . /home/galaxy/venv/bin/activate && pip install bioblend
  
  # modified supervisor conf file
  ADD galaxy_build.conf /etc/galaxy/
  
negative.code: RUN apt-get -qq update && apt-get install --no-install-recommends -y apt-transport-https software-properties-common && \
      apt-add-repository -y ppa:bibi-help/bibitools && \
      apt-get -qq update && \
      apt-get install --no-install-recommends -y rnashapes && \
      apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
      . /home/galaxy/venv/bin/activate && pip install bioblend
  
  RUN install-repository "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name rnabob --panel-section-name RNATools" \
      "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name text_processing --panel-section-id textutil" \
  