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galaxyproject / ephemeris

Library for managing Galaxy plugins - tools, index data, and workflows.
https://ephemeris.readthedocs.org/
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Add tool_deps tool to allow triggering installation of local tool dep… #130

Closed innovate-invent closed 4 years ago

innovate-invent commented 5 years ago

…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

mvdbeek commented 5 years ago

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 commented 5 years ago

@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 commented 5 years ago

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 commented 5 years ago

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 commented 4 years ago

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.