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README.md
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README.md

phylesystem-1

If you are not an open tree developer working on the api or tools that read from the "raw" git repo), you can probably ignore this repository.

This is a repository of phylogenetic studies used by the Open Tree of Life project. The files are in the HoneyBadgerFish 1.2 NexSON syntax.

This repository is the backend datastore of the Open Tree api web services.

Currently we do not support pull requests to this repo (though we hope to soon).

We have not decided on the final naming scheme for shards in the phylesystem repository (if we use a sharding strategy). Additional phylesystem-suffix repositories may be added.

The top-level phylesystem repository will hold git submodule links to each of the shards.

History

The initial state of the repository was created by downloading studies from phylografter to update the old-phylesystem repository.

Then (assuming the directory structure):

somepath/old-phylesystem
somepath/peyotl

then you can create the content of this directory by:

cd somepath/old-phylesystem
python bin/refresh_nexsons_from_phylografter.py -v
cd ../peyotl
mkdir -p ../phylesystem/phylesystem-0/study
mkdir ../migration2phylesystem-1
python dev/migrate_testing_phylesystem.py ../old-phylesystem ../phylesystem/phylesystem-1 ../migration2phylesystem-1 >migration-out.txt 2>migration-err.txt 

License

Some of the data in this repository is released under the Create Commons Zero 1.0 Universal waiver; the rest is released to the public without any particular license or waiver.

When using any of this data please cite the original source using a bibliographic reference and DOI for the study's publication, as given in each file, and Treebase or other data deposit identifier if available.

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