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comparison toolfactory/docker/Dockerfile @ 46:f8700bed1e17 draft

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author fubar
date Tue, 18 Aug 2020 08:25:43 -0400
parents f8c1694190f0
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45:668c37cc8962 46:f8700bed1e17
1 # Galaxy - Toolshed Docker image 1 # Galaxy - Toolshed Docker image
2 # Derived from bgruening stable galaxy 2 # Derived from bgruening stable galaxy
3 # VERSION 0.2 3 # VERSION 0.2
4 # patches startup so the below will install a workflow dropped into $GALAXY_ROOT/workflows 4 # patches startup so the below will install a workflow dropped into $GALAXY_ROOT/workflows
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 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
6 FROM bgruening/galaxy-stable 6 FROM quay.io/bgruening/galaxy:20.05
7 MAINTAINER Ross Lazarus ross.lazarus@gmail.com 7 MAINTAINER Ross Lazarus ross.lazarus@gmail.com
8 8
9 ENV GALAXY_CONFIG_BRAND=ToolFactory 9 ENV GALAXY_CONFIG_BRAND=ToolFactory
10 ENV GALAXY_LOGGING="full" 10 ENV GALAXY_LOGGING="full"
11 ADD tfwelcome.html /export/welcome.html
12 # RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed'
13 RUN mkdir -p /tftools \
14 && mkdir -p /tftools/toolfactory \
15 && mkdir -p /tftools/planemo_test
11 16
12 # RUN apt-get update -y && apt-get install -y build-essential gcc apt-utils 17 ADD ./tftools/toolfactory /tftools/toolfactory
13 # needed for planemo build 18 ADD ./tftools/tf_tool_conf.xml /tftools/tf_tool_conf.xml
19 ADD ./tftools/planemo_test /tftools/planemo_test
20 ADD TF_example_wf.ga /tftools/TF_example_wf.ga
14 21
15 RUN /galaxy_venv/bin/python -m pip install --upgrade pip 22 ADD my_tool_list.yml /tftools/toolfactory_tools.yaml
16 # RUN /galaxy_venv/bin/python -m pip install planemo
17 23
18 # RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed' 24 ENV GALAXY_AUTO_UPDATE_TOOLS=/tftools/toolfactory_tools.yaml
19 ADD my_tool_list.yml $GALAXY_ROOT/config/toolfactory_tools.yaml 25 # NOTE above does work but takes 1-2 minutes
20 ENV GALAXY_AUTO_UPDATE_TOOLS=$GALAXY_ROOT/config/toolfactory_tools.yaml
21 26
27 # ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/tf_tool_conf.xml,config/shed_tool_conf.xml.sample
28 #ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=/tftools/tf_tool_conf.xml,config/tool_conf.xml.sample
29 # works but does not install dependencies
22 # Add workflows to the Docker image 30 # Add workflows to the Docker image
23 RUN mkdir -p $GALAXY_ROOT/workflows 31
24 ADD TF_example_wf.ga $GALAXY_ROOT/workflows/TF_example_wf.ga 32 ENV $GALAXY_DEFAULT_ADMIN_USER="admin"
33 # ensure triggering post-start-actions.sh
34
35 ADD tftools/datatypes_conf.xml $GALAXY_ROOT/conf/datatypes_conf.xml.sample
25 ADD post-start-actions.sh /export/post-start-actions.sh 36 ADD post-start-actions.sh /export/post-start-actions.sh
37 ADD post-start-actions.sh $GALAXY_ROOT/config/post-start-actions.sh
38
26 RUN chmod a+xr /export/post-start-actions.sh \ 39 RUN chmod a+xr /export/post-start-actions.sh \
27 && chmod a+xr $GALAXY_ROOT/workflows/TF_example_wf.ga 40 && chmod a+xr /tftools/TF_example_wf.ga \
28 41 && chmod a+xr $GALAXY_ROOT/config/post-start-actions.sh
29 # Add Galaxy interactive tours 42 # Add Galaxy interactive tours
30 # ADD ./rna-workbench-tours/* $GALAXY_ROOT/config/plugins/tours/ 43 # ADD ./rna-workbench-tours/* $GALAXY_ROOT/config/plugins/tours/
31 # Add data library definition file 44 # Add data library definition file
32 # ADD library_data.yaml $GALAXY_ROOT/library_data.yaml 45 # ADD library_data.yaml $GALAXY_ROOT/library_data.yaml
33 # cleanup dance 46
34 RUN apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \ 47 VOLUME ["/export/", "/data/", "/var/lib/docker"]
35 && find $GALAXY_ROOT/ -name '*.pyc' -delete | true \
36 && find /usr/lib/ -name '*.pyc' -delete | true \
37 && find /var/log/ -name '*.log' -delete | true \
38 && find $GALAXY_VIRTUAL_ENV -name '*.pyc' -delete | true \
39 && rm -rf /tmp/* /root/.cache/ /var/cache/* $GALAXY_ROOT/client/node_modules/ $GALAXY_VIRTUAL_ENV/src/ /home/galaxy/.cache/ /home/galaxy/.npm
40 ENV GALAXY_DEFAULT_ADMIN_USER=''
41 VOLUME ["/export/"]
42 EXPOSE :80 48 EXPOSE :80
43 EXPOSE :21 49 EXPOSE :21
44 EXPOSE :8800 50 EXPOSE :8800
51
45 CMD ["/usr/bin/startup"] 52 CMD ["/usr/bin/startup"]
46