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Improvement Description
I finally was able to clean up Siavash's source code and created a bioconda recipe for SEPP, producing the packages at https://anaconda.org/bioconda/sepp
Note that this package does NOT contain the default Greengenes 13.8 99% reference (which consists of three files a) alignment b) tree c) info file.) In the future, we also want to support alternative references like SILVA.
Proposed Behavior
I wonder how we best do this? I see the following options:
create conda reference packages for GG and / or SILVA pro: no changes to current behaviour of qiime2 con: where to host? would bioconda accept that?
provide as qiime2 Data resources pro: smaller downloads when qiime2 gets installed, easy to host con: user need to do extra work when a) install and b) execute since file paths for all three files need to be provided
Just wondering, what will be your thoughts about adding a command/method to download the available references and set them in your environment? Something like: qiime fragment-insertion --show-available-references; qiime fragment-insertion --download-reference XXX; qiime fragment-insertion --show-local-references-locations ...
I think I am leaning towards option #2. @ebolyen and I recently discussed some potential machinery for fetching and caching data assets on a per-deployment basis, which might ease the user-burden (so, something similar to what @antgonza is proposing).
Improvement Description
I finally was able to clean up Siavash's source code and created a bioconda recipe for SEPP, producing the packages at https://anaconda.org/bioconda/sepp
Note that this package does NOT contain the default Greengenes 13.8 99% reference (which consists of three files a) alignment b) tree c) info file.) In the future, we also want to support alternative references like SILVA.
Proposed Behavior
I wonder how we best do this? I see the following options:
pro: no changes to current behaviour of qiime2
con: where to host? would bioconda accept that?
Data resources
pro: smaller downloads when qiime2 gets installed, easy to host
con: user need to do extra work when a) install and b) execute since file paths for all three files need to be provided
Questions
Any thoughts @thermokarst @antgonza ?
References
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