[MRG] Update the sourmash doc with gather and tax #79
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| ``` | ||
| curl -L https://osf.io/4f8n3/download -o genbank-k31.lca.json.gz | ||
| gunzip genbank-k31.lca.json.gz | ||
| curl -JLO https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-reps.k31.lca.json.gz |
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assuming we're running this on farm, you can just point people at /group/ctbrowngrp/sourmash-db/gtdb-rs214!
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also, with gather, no need to use the LCA database (which is bigger memory, tho maybe faster). could just as easily use the regular zip.
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assuming we're running this on farm, you can just point people at /group/ctbrowngrp/sourmash-db/gtdb-rs214!
Would that be a good time to introduce ln -s as well?
also, with gather, no need to use the LCA database (which is bigger memory, tho maybe faster). could just as easily use the regular zip.
I did add a Bonus goal at the end of the document to use the standard zip database, I think I should switch them around. Introduce the zip db in the document and add a bonus about using other database types...?
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assuming we're running this on farm, you can just point people at /group/ctbrowngrp/sourmash-db/gtdb-rs214!
Would that be a good time to introduce
ln -sas well?
sure!
also, with gather, no need to use the LCA database (which is bigger memory, tho maybe faster). could just as easily use the regular zip.
I did add a Bonus goal at the end of the document to use the standard zip database, I think I should switch them around. Introduce the zip db in the document and add a bonus about using other database types...?
zip better. Not sure why other database types needed here, but sure, in the bonus section... :)
Co-authored-by: C. Titus Brown <titus@idyll.org>
Fixes #61
Fixes #28
Changed the
lcacommand togather. Added some detailed text and a bonus task.