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FROM quay.io/galaxyproject/galaxy-min:23.2.1
ARG SERVER_DIR
# switch to root
USER root
RUN apt-get -qq update && \
apt-get install -y git pkg-config default-libmysqlclient-dev gcc ca-certificates mercurial
# Clone Pyclone-VI tools from GitHUb
RUN git clone https://github.com/jCHENEBY/galaxy-tool-pyclone-vi.git /galaxy/server/tools/pyclone_vi
RUN chown -R galaxy:galaxy /galaxy/server/tools/pyclone_vi
# Clone Cellular prevalence graph tools from GitHub
RUN git clone --branch v1.2.3 https://github.com/jCHENEBY/galaxy-tool-plot-cluster-prevalence.git /galaxy/server/tools/plot_clusters_prevalence
#COPY plot_clusters_prevalence /galaxy/server/tools/plot_clusters_prevalence/
RUN chown -R galaxy:galaxy /galaxy/server/tools/plot_clusters_prevalence
# Clone Export timeline to cBioportal tools from GitHub
RUN git clone https://github.com/jCHENEBY/galaxy-tool-export-cbioportal-timeline.git /galaxy/server/tools/export_cbioportal_timeline
#COPY export_cbioportal_timeline /galaxy/server/tools/export_cbioportal_timeline/
RUN chown -R galaxy:galaxy /galaxy/server/tools/export_cbioportal_timeline
# Clone Export image to cBioportal tools from GitHub
RUN git clone https://github.com/jCHENEBY/galaxy-tool-export-cbioportal-image.git /galaxy/server/tools/export_cbioportal_image
#COPY export_cbioportal_image /galaxy/server/tools/export_cbioportal_image/
RUN chown -R galaxy:galaxy /galaxy/server/tools/export_cbioportal_image
# Clone Query tabular fro IUC
RUN hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/query_tabular /galaxy/server/tools/query_tabular
RUN chown -R galaxy:galaxy /galaxy/server/tools/query_tabular
## Copy pyclone_vi tool
#COPY tools/pyclone_vi /galaxy/server/tools/pyclone_vi
#RUN chown -R galaxy:galaxy /galaxy/server/tools/pyclone_vi
#
## Copy Cellular prevalence graph tool
#COPY tools/plot_clusters_prevalence /galaxy/server/tools/plot_clusters_prevalence
#RUN chown -R galaxy:galaxy /galaxy/server/tools/plot_clusters_prevalence
COPY config/tool_conf.xml /galaxy/server/config/tool_conf.xml
RUN chown galaxy:galaxy /galaxy/server/config/tool_conf.xml
# Create database directory
RUN mkdir /database
RUN chown -R galaxy:galaxy /database
# Create a shared config directory
RUN mkdir /config
RUN chown -R galaxy:galaxy /config
# Create a shared study directory
RUN mkdir /study
RUN chown 777 /study
# Import the entrypoint script
COPY entrypoint.sh /entrypoint.sh
RUN chmod +x /entrypoint.sh
RUN chown galaxy:galaxy /entrypoint.sh
# switch back to galaxy
USER galaxy
RUN sed -i 's/static_enabled\: false/static_enabled: true/' config/galaxy.yml
RUN sed -i 's/bind\: 0.0.0.0\:8080/bind: 0.0.0.0:8081/' config/galaxy.yml
RUN sed -i 's|tool_config_file: /galaxy/server/config/tool_conf.xml.sample|tool_config_file: /galaxy/server/config/tool_conf.xml|' config/galaxy.yml
# Configure Galaxy for external Docker volumes
RUN sed -i 's|data_dir: /galaxy/server/database|data_dir: /database|' config/galaxy.yml
RUN sed -i 's|^[[:space:]]*file_path:.*|#&|' config/galaxy.yml
RUN sed -i 's|^[[:space:]]*job_working_directory:.*|#&|' config/galaxy.yml
RUN sed -i 's|^[[:space:]]*tool_data_path:.*|#&|' config/galaxy.yml
RUN sed -i 's|^[[:space:]]*tool_dependency_dir:.*|#&|' config/galaxy.yml
# Setup PyClone
RUN pip install pandas matplotlib seaborn numpy scipy galaxy-lib numba dsnparse mysqlclient python-dotenv