This directory is a Genspectrum-maintained nextclade server, created using the docs: https://github.com/nextstrain/nextclade_data/blob/master/docs/dataset-server-maintenance.md.
How to add new datasets?
- Create a dataset following nextclade's instructions.
- Update the
index.json
: this should include the details from each pathogen.json folder, additionally theindex.json
expects datasets to be versioned. For simplicity set version to unreleased and keep each dataset in a subdirectory calledunreleased
. - Zip the contents of the dataset into
dataset.zip
- this is what will be downloaded by nextclade and unzipped prior to use.
for i in {1..8}; do
rm -rf dataset.zip
cd seg$i/unreleased
zip -r dataset.zip *
cd -
done
Note that steps 2 and 3 are performed automatically by the CI when you create an official nextclade dataset, using the rebuild script.
Download H5N1 datasets as follows:
for i in {1..8}; do
nextclade_dataset_name=flu/h5n1/seg$i
nextclade_dataset_server=https://raw.githubusercontent.com/genspectrum/nextclade-datasets/main/data
nextclade3 dataset get --name $nextclade_dataset_name --server $nextclade_dataset_server --output-dir output$i
done