FROM bgruening/galaxy-stable

MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com

ENV GALAXY_CONFIG_BRAND MyGalaxy
ENV GALAXY_CONFIG_DATABASE_CONNECTION postgresql://galaxy:galaxy@localhost:5432/galaxy
ENV GALAXY_CONFIG_TOOL_CONFIG_FILE config/tool_conf.xml.sample,/data/local_tool_conf.xml
ENV GALAXY_CONFIG_ADMIN_USERS admin@galaxy.org
ENV GALAXY_CONFIG_MASTER_API_KEY HSNiugRFvgT574F43jZ7N9F3
ENV GALAXY_CONFIG_SANITIZE_ALL_HTML False
ENV GALAXY_SLOTS 28

WORKDIR /galaxy-central

RUN apt-get update && apt-get install -y libtbb2 netcat screen


# Mark folders as imported from the host.
VOLUME ["/export/", "/data/", "/var/lib/docker"]

ADD cloud_tools.yml $GALAXY_ROOT/cloud_tools.yaml
ADD tools /tools
ADD makelinks.sh /makelinks.sh
RUN /makelinks.sh
ADD workflows /workflows
ADD local_tool_conf.xml /data/local_tool_conf.xml
ADD datatypes_conf.xml $GALAXY_ROOT/config/datatypes_conf.xml
ADD data_managers.yml $GALAXY_ROOT/data_managers.yml
ADD install_workflow_wrapper.sh /install_workflow_wrapper.sh
ADD launcher.py /launcher.py
ADD hg38.fa $GALAXY_ROOT/tool-data/hg38/seq/hg38.fa
ADD job_conf.xml $GALAXY_ROOT/config/job_conf.xml

RUN install-tools $GALAXY_ROOT/cloud_tools.yaml

RUN chmod +x /install_workflow_wrapper.sh; /install_workflow_wrapper.sh

RUN startup_lite && \
    /tool_deps/_conda/bin/install_tool_deps -v -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD  -g http://localhost:8080 -t /data/local_tool_conf.xml && \
    /tool_deps/_conda/bin/run-data-managers -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD  -g http://localhost:8080 --config data_managers.yml && \
    sleep 60 && \
    /tool_deps/_conda/bin/workflow-install -v -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD -g http://localhost:8080 -w /workflows/ && \
    /tool_deps/_conda/bin/conda install -y simplejson && \
    /tool_deps/_conda/bin/conda clean --tarballs


EXPOSE :80
EXPOSE :21
EXPOSE :8800

## Autostart script that is invoked during container start
CMD ["/usr/bin/startup"]