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galaxy-iuc / standards

Documentation for standards and best practices from the Galaxy IUC
http://galaxy-iuc-standards.readthedocs.io/en/latest/
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Tool dependency packages section out of date #70

Closed elichad closed 2 years ago

elichad commented 2 years ago

https://github.com/galaxy-iuc/standards/blob/master/docs/best_practices/tool_xml.rst#tool-dependency-package

If you are using perl/ruby/python/R packages, use the corresponding *_environment tags to depend on a specific version of Perl/Ruby ...

  1. I think this section is out of date. I can't find any *_environment tags in the tool docs except set_environment which is ignored by conda anyway, and it looks like the currently recommended syntax is more like <requirement type="package" version="2.15.1">R</requirement>
  2. Is this a 'can' or 'should' piece of guidance? e.g. if my packages support all current versions of Python, should I still specify a particular version?
nsoranzo commented 2 years ago

Thanks @elichad for reporting the issue! 1) Yes, I'll open a PR to remove that section 2) If your requirement is a Python/R/... package, you don't usually need to specify an additional requirement for the language version. If instead you are shipping a script with your tool, it's recommended to add a <requirement /> for the language with a version.

Hope that helps!