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1 # Galaxy - Toolshed Docker image
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2 # Derived from bgruening stable galaxy
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3 # VERSION 0.2
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4 # patches startup so the below will install a workflow dropped into $GALAXY_ROOT/workflows
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5 # use docker run -p 8080:80 -d -e GALAXY_AUTO_UPDATE_WORKFLOWS=/galaxy-central/workflows/TF_sample_wf.ga -v /home/ubuntu/galaxy_storage/:/export/ toolfactory
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6 FROM bgruening/galaxy-stable
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7 MAINTAINER Ross Lazarus ross.lazarus@gmail.com
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8
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9 ENV GALAXY_CONFIG_BRAND=ToolFactory
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10 ENV GALAXY_LOGGING="full"
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11
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12 # RUN apt-get update -y && apt-get install -y build-essential gcc apt-utils
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13 # needed for planemo build
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14
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15 RUN /galaxy_venv/bin/python -m pip install --upgrade pip
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16 # RUN /galaxy_venv/bin/python -m pip install planemo
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17
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18 # RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed'
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19 ADD my_tool_list.yml $GALAXY_ROOT/config/toolfactory_tools.yaml
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20 ENV GALAXY_AUTO_UPDATE_TOOLS=$GALAXY_ROOT/config/toolfactory_tools.yaml
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21
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22 # Add workflows to the Docker image
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23 RUN mkdir -p $GALAXY_ROOT/workflows
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24 ADD TF_example_wf.ga $GALAXY_ROOT/workflows/TF_example_wf.ga
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25 ADD post-start-actions.sh /export/post-start-actions.sh
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26 RUN chmod a+xr /export/post-start-actions.sh \
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27 && chmod a+xr $GALAXY_ROOT/workflows/TF_example_wf.ga
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28
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29 # Add Galaxy interactive tours
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30 # ADD ./rna-workbench-tours/* $GALAXY_ROOT/config/plugins/tours/
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31 # Add data library definition file
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32 # ADD library_data.yaml $GALAXY_ROOT/library_data.yaml
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33 # cleanup dance
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34 RUN apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \
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35 && find $GALAXY_ROOT/ -name '*.pyc' -delete | true \
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36 && find /usr/lib/ -name '*.pyc' -delete | true \
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37 && find /var/log/ -name '*.log' -delete | true \
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38 && find $GALAXY_VIRTUAL_ENV -name '*.pyc' -delete | true \
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39 && rm -rf /tmp/* /root/.cache/ /var/cache/* $GALAXY_ROOT/client/node_modules/ $GALAXY_VIRTUAL_ENV/src/ /home/galaxy/.cache/ /home/galaxy/.npm
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40 ENV GALAXY_DEFAULT_ADMIN_USER=''
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41 VOLUME ["/export/"]
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42 EXPOSE :80
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43 EXPOSE :21
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44 EXPOSE :8800
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45 CMD ["/usr/bin/startup"]
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46
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