anchor.diff:  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/*
  -
  -
  -# The following line is a workaround for an issue on Ubuntu with AUFS
  -# for details visit: https://github.com/docker/docker/issues/783
  -#RUN mkdir /etc/ssl/private-copy; mv /etc/ssl/private/* /etc/ssl/private-copy/; rm -r /etc/ssl/private; mv /etc/ssl/private-copy /etc/ssl/private; chmod -R 0700 /etc/ssl/private; chown -R postgres /etc/ssl/private
  -
  +    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" \
  
positive.code: 
  # 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
  
  RUN start_galaxy_for_build && . $GALAXY_VIRTUALENV/bin/activate && python -u setup_data_libraries.py && 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
  
  # 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"]
  
negative.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" \
      "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name rnashapes --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 | tar xz && cp -r galaxytools-master/visualisations/* config/plugins/visualizations/ && rm -rf ./galaxytools-master
  
  # modified supervisor conf file
  ADD galaxy_build.conf /etc/galaxy/
  