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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 quay.io/bgruening/galaxy:20.05
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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 ADD tfwelcome.html /export/welcome.html
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12 # RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed'
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13 RUN mkdir -p /tftools \
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14 && mkdir -p /tftools/toolfactory \
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15 && mkdir -p /tftools/planemo_test
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16
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17 ADD ./tftools/toolfactory /tftools/toolfactory
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18 ADD ./tftools/tf_tool_conf.xml /tftools/tf_tool_conf.xml
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19 ADD ./tftools/planemo_test /tftools/planemo_test
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20 ADD TF_example_wf.ga /tftools/TF_example_wf.ga
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21
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22 ADD my_tool_list.yml /tftools/toolfactory_tools.yaml
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23
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24 ENV GALAXY_AUTO_UPDATE_TOOLS=/tftools/toolfactory_tools.yaml
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25 # NOTE above does work but takes 1-2 minutes
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26
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27 # ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/tf_tool_conf.xml,config/shed_tool_conf.xml.sample
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28 #ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=/tftools/tf_tool_conf.xml,config/tool_conf.xml.sample
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29 # works but does not install dependencies
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30 # Add workflows to the Docker image
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31
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32 ENV $GALAXY_DEFAULT_ADMIN_USER="admin"
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33 # ensure triggering post-start-actions.sh
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34
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35 ADD tftools/datatypes_conf.xml $GALAXY_ROOT/conf/datatypes_conf.xml.sample
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36 ADD post-start-actions.sh /export/post-start-actions.sh
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37 ADD post-start-actions.sh $GALAXY_ROOT/config/post-start-actions.sh
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38
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39 RUN chmod a+xr /export/post-start-actions.sh \
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40 && chmod a+xr /tftools/TF_example_wf.ga \
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41 && chmod a+xr $GALAXY_ROOT/config/post-start-actions.sh
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41
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42 # Add Galaxy interactive tours
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43 # ADD ./rna-workbench-tours/* $GALAXY_ROOT/config/plugins/tours/
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44 # Add data library definition file
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45 # ADD library_data.yaml $GALAXY_ROOT/library_data.yaml
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46
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47 VOLUME ["/export/", "/data/", "/var/lib/docker"]
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48 EXPOSE :80
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49 EXPOSE :21
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50 EXPOSE :8800
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51
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52 CMD ["/usr/bin/startup"]
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