https://github.com/ctb/2021-sourmash-datasette
Exploring datasette for exploring microbial taxonomy analyses of metagenomes wit hsourmash
https://github.com/ctb/2021-sourmash-datasette
sourmash sqlite
Last synced: 3 months ago
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Exploring datasette for exploring microbial taxonomy analyses of metagenomes wit hsourmash
- Host: GitHub
- URL: https://github.com/ctb/2021-sourmash-datasette
- Owner: ctb
- Created: 2021-09-05T16:50:00.000Z (almost 5 years ago)
- Default Branch: latest
- Last Pushed: 2021-09-05T17:36:50.000Z (almost 5 years ago)
- Last Synced: 2025-06-07T20:06:37.812Z (about 1 year ago)
- Topics: sourmash, sqlite
- Language: Python
- Homepage:
- Size: 36.1 KB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 2021-sourmash-datasette
Exploring sourmash 'gather' and 'taxonomy' output with
[datasette](https://datasette.io/).
## Quickstart
First install [datasette](https://datasette.io/) and
[csvs-to-sqlite](https://datasette.io/tools/csvs-to-sqlite).
This can be done with conda or mamba:
```
conda env create -n datasette -f environment.yml
conda activate datasette
```
Then run:
```
# convert sourmash gather/sourmash tax output lineages into their own cols
./make-db.sh
# run datasette!
datasette gathertax.db --static sourmash:static/ -o
```
Finally, go to `/sourmash/index.html` at your datasette site - by
default, it should be at
[127.0.0.1:8001/sourmash/index.html](http://127.0.0.1:8001/sourmash/index.html).