Add tool_deps tool to allow triggering installation of local tool dep…

[innovate-invent]

…endencies

The contribution docs don't detail how to do tests. This tool requires that a tool has already been manually installed into galaxy.

It also isn't clear how to provide a command line wrapper to execute the python script

[bgruening]

Thanks @innovate-invent!

[mvdbeek]

This requires either the tool xml file or a tool_conf.xml, neither of which are formats we deal with in ephemeris and that are very local to Galaxy. I'd suggest a simple yaml list of tool ids.

[innovate-invent]

@mvdbeek It does take a list of tool ids on the command line. The tool_conf.xml support is useful when deploying a container and ephemeris is connecting to localhost with direct access to galaxies filesystem.

[mvdbeek]

I understand the utility, but in principle that's not the scope of ephemeris. Still this mostly works via the API, so if you can add loading a plain list of tool ids via yaml.safe_load and make that the default for -t (in line with other commands expecting a yaml file with -t) I'm OK to merge this.

[mvdbeek]

There are some linting errors now (https://travis-ci.org/galaxyproject/ephemeris/jobs/543810023#L475), the other failures should have been temporary and unrelated.

[innovate-invent]

The current lint failure is not relevant to this project. The security implication is that it could fill RAM and crash the system if a malicious xml file is provided.