|
42
|
1 # Galaxy - Toolshed Docker image
|
|
|
2 # Derived from bgruening stable galaxy
|
|
|
3 # VERSION 0.2
|
|
|
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
|
|
|
6 FROM bgruening/galaxy-stable
|
|
|
7 MAINTAINER Ross Lazarus ross.lazarus@gmail.com
|
|
|
8
|
|
|
9 ENV GALAXY_CONFIG_BRAND=ToolFactory
|
|
|
10 ENV GALAXY_LOGGING="full"
|
|
|
11
|
|
|
12 # RUN apt-get update -y && apt-get install -y build-essential gcc apt-utils
|
|
|
13 # needed for planemo build
|
|
|
14
|
|
|
15 RUN /galaxy_venv/bin/python -m pip install --upgrade pip
|
|
|
16 # RUN /galaxy_venv/bin/python -m pip install planemo
|
|
|
17
|
|
|
18 # RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed'
|
|
|
19 ADD my_tool_list.yml $GALAXY_ROOT/config/toolfactory_tools.yaml
|
|
|
20 ENV GALAXY_AUTO_UPDATE_TOOLS=$GALAXY_ROOT/config/toolfactory_tools.yaml
|
|
|
21
|
|
|
22 # Add workflows to the Docker image
|
|
|
23 RUN mkdir -p $GALAXY_ROOT/workflows
|
|
|
24 ADD TF_example_wf.ga $GALAXY_ROOT/workflows/TF_example_wf.ga
|
|
|
25 ADD post-start-actions.sh /export/post-start-actions.sh
|
|
|
26 RUN chmod a+xr /export/post-start-actions.sh \
|
|
|
27 && chmod a+xr $GALAXY_ROOT/workflows/TF_example_wf.ga
|
|
|
28
|
|
|
29 # Add Galaxy interactive tours
|
|
|
30 # ADD ./rna-workbench-tours/* $GALAXY_ROOT/config/plugins/tours/
|
|
|
31 # Add data library definition file
|
|
|
32 # ADD library_data.yaml $GALAXY_ROOT/library_data.yaml
|
|
|
33 # cleanup dance
|
|
|
34 RUN apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \
|
|
|
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
|
|
|
43 EXPOSE :21
|
|
|
44 EXPOSE :8800
|
|
|
45 CMD ["/usr/bin/startup"]
|
|
|
46
|
