On Mon, Aug 26, 2013 at 11:48 AM, John Chilton <chil...@msi.umn.edu> wrote:

> I think it is interesting that there was push back on providing
> infrastructure (tool actions) for obtaining CBL from github and
> performing installs based on it because it was not in the tool shed
> and therefore less reproducible, but the team believes infrastructure
> should be put in place to support pypi.

Well, first, I'm not sure what "the team" believes, I'm stating what I
believe and engaging in a discussion with "the community". At some
point this should evolve into what we are actually going to do and be
codified in a spec as a Trello card, which is even then not set in

Second, I'm not suggesting we depend on PyPI. The nice thing about the
second format I proposed on galaxy-dev is that we can easily parse out
the URL and archive that file. Then someday we could provide a
fallback repository where if the PyPI URL no longer works we still
have it stored.

> I think we all value reproduciblity here, but we make different
> calculations on what is reproducible. I think in terms of implementing
> the ideas James has laid out or similar things I have proposed, it
> might be beneficial to have some final answers on what external
> resources are allowed - both for obtaining a Galaxy IUC gold star and
> for the tool shed providing infrastructure to support their usage.

My focus is ensuring that we can archive things that pass through the
toolshed. Tarballs from *anywhere* are easy enough to deal with.
External version control repositories are a bit more challenging,
especially when you are pulling just a particular file out, so that's
where things got a little hinky for me.

Since we don't have the archival mechanism in place yet anyway, this
is more a philosophical discussion and setting the right precedent.

And yes, keeping an archive of all the software in the world is a
scary prospect, though compared to the amount of data we currently
keep for people it is a blip. And I'm not sure how else we can really
achieve the level of reproducibility we desire.
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