Integrating non-Tool Shed tools into the container

We recommend to use the Main Galaxy Tool Shed for all your tools and workflows that you would like to share. In rare situations where you cannot share your tools but still want to include them into your Galaxy Docker instance, please follow the next steps.

• Get your tools into the container.

  Mount your tool directory into the container with a separate -v /home/user/my_galaxy_tools/:/local_tools .

• Create a tool_conf.xml file for your tools.

  This should look similar to the main tool_conf.xml file, but references your tools from the new directory. In other words a tool entry should look like this <tool file="/local_tools/application_foo/foo.xml" /> . Your tool_conf.xml should be available from inside of the container. We assume you have it stored under /local_tools/my_tools.xml .

• Add the new tool config file to the Galaxy configuration.

  To make Galaxy aware of your new tool configuration file you need to add the path to tool_config_file , which is set to /etc/galaxy/tool_conf.xml . You can do this during container start by setting the environment variable -e GALAXY_CONFIG_TOOL_CONFIG_FILE=/etc/galaxy/tool_conf.xml,/local_tools/my_tools.xml .