[MRG] Update the sourmash doc with gather and tax#79
[MRG] Update the sourmash doc with gather and tax#79ccbaumler wants to merge 2 commits intodib-lab:mainfrom
Conversation
| ``` | ||
| 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 |
There was a problem hiding this comment.
assuming we're running this on farm, you can just point people at /group/ctbrowngrp/sourmash-db/gtdb-rs214!
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
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...?
There was a problem hiding this comment.
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>
2 participants
Fixes #61
Fixes #28
Changed the
lcacommand togather. Added some detailed text and a bonus task.