I am attempting to create a docker image for a “flavor” of galaxy for one of my colleagues. Just to test things out, I’ve tried building from the bgruening/galaxy-stable image, and I’m only adding one tool from the tool shed: peptideshaker.
The image builds without issue, and even launches, but the peptideshaker tools do not appear in the sidebar of the galaxy page exposed at port 8080.
Here is my docker file:
FROM bgruening/galaxy-stable:latest MAINTAINER Björn A. Grüning, email@example.com ENV GALAXY_CONFIG_BRAND PeptideShaker WORKDIR /galaxy-central RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed' # Install tools ADD my_test_list.yml $GALAXY_ROOT/tools.yaml RUN install-tools $GALAXY_ROOT/tools.yaml # Mark folders as imported from the host. VOLUME ["/export/", "/data/", "/var/lib/docker"] # Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy) EXPOSE :80 EXPOSE :21 EXPOSE :8800 # Autostart script that is invoked during container start CMD ["/usr/bin/startup"]
and the file
--- api_key: admin galaxy_instance: http://localhost:8080 tools: - name: peptideshaker owner: galaxyp tool_panel_section_label: "PeptideShaker" revisions: - 3ec27b4cee7c
When I check to see if the peptideshaker tool is installed (as an admin), the tools are installed. However, I can’t see them in the sidebar, nor can I see the “PeptideShaker” section that was meant to be created, and the tools do not show up in the search in the sidebar.
I’m sure others have run into this issue. Does anyone know how to resolve it?
Thanks in advance!