New open ref workflow - do not merge

[josenavas]

@gregcaporaso this is the PR with the new OR workflow

[gregcaporaso]

I think this would be clearer if you did this as while len(seq_generators) > 0, rather than creating a separate done variable. Would that work? It'd let you drop the if/else, which would be nice.

[ghost]

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1599/

[gregcaporaso]

Just a couple of comments @josenavas, looks good!

I guess we need to figure out what to do with this code... We need it for EMP, but it will never end up in a QIIME release in this form (since it would be re-written for QIIME 2). I think we should add it here, and that way you can cite QIIME 1.9.0-dev with a specific commit hash, and if we want to explore this approach further it will be accessible.

[gregcaporaso]

Failures all look related to R packages so we'll see what happens when/if you push changes based on my comments.

[josenavas]

Thanks for the review @gregcaporaso
I agree, merging here so we can point to it is the best route...

[ghost]

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1600/

[ghost]

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1601/

[gregcaporaso]

closing in favor of #1958.