Michal Stolarczyk

@KevinMenden, I can help put together the refgenie asset recipes for the missing asset types. Where can I find commands used to create these?

interesting, `pypiper.PipelineManager` object destruction does not seem to help here

rn6 genome description has that info: http://refgenomes.databio.org/#rn6 the exact source URL can be found here: https://github.com/databio/databio_genomes/blob/master/asset_pep/recipe_inputs.csv

no change. I assigned it to this milestone https://github.com/refgenie/refgenie/milestone/6 in July for some reason

That's what we've done. The "MapReduce" framework is now supported in the development version of refgenie and is documented here: http://refgenie.databio.org/en/dev/build/#build-assets-concurrently. We will release this early this week. In the...

> I'm assuming (and some initial testing seems to confirm) that dependencies of the indexing operations (fasta, fasta_txome) do need to exist in the central database before the indexing operations....

> Run a reduce for each assembly That's not possible. If you use `--reduce` flag, genome/asset specifications are disregarded. Reduce step is run globally. This needs to be either clarified...

> All of fasta_txome, hisatw_index, bowtie_index etc just need the reference genome to exist That's what I was getting at in my previous comment. `fasta_txome` doesn't require `fasta` to exist,...

So this boils down to two rules for running `refgenie build --reduce`: 1. Run only one `refgenie build --reduce` at a time 2. Run only when there are no `refgenie...

> Ahh, I'd thought that each assembly needed a /fasta in place as a starting point (to establish the SHA digest) oh, wait you're right :) But build other top-level...