fix get_gg and get_silva makefile directives about pretrained-feature-classifiers HOT 5 OPEN

As far as I can tell these are still needed to populate the ./input folder, as train.sh only takes .qza files as input.

get_silva.sh uses qiime rescript get-silva-data but get_gg.sh uses wget for everything, thus the cross ref.

Am I missing something? Is there a newer version in production?

from pretrained-feature-classifiers.

@colinbrislawn, yes, there is a newer version in production, looks like the dangling draft PR is still outstanding, here:

#10
One of the pieces that I started working on while setting that PR up was either inlining the get_* steps, or, fixing up the makefile to properly declare the "order of operations." I have no real preference, I suppose, but as it stands I think we need to do something different (right now that PR just settles on documenting the steps more clearly).

I edited my original issue above to clarify where my mind was at when I filed this issue, let me know if that makes more sense.

from pretrained-feature-classifiers.

xref bokulich-lab/RESCRIPt#124

from pretrained-feature-classifiers.

@colinbrislawn is correct, these are still relevant to this project, get_silva.sh just uses rescript now.

Even with RESCRIPt, the data download might not be necessary with each QIIME 2 release (as it only needs to be run each time a new database version is released). Hence keeping it separate.

from pretrained-feature-classifiers.

(fixing the makefile dependency steps is probably the easiest option here - ill update this issue title to make that more clear)

from pretrained-feature-classifiers.