167 sourmash clustering does not work with dynamic sample ids - Githubissues

Clinical-Genomics-Lund / bonsai

Visualize and analyze resistance and outbreak of bacterial pathogen

https://bonsai-wgs.readthedocs.io/en/latest/

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167 sourmash clustering does not work with dynamic sample ids #168

Closed mhkc closed 5 months ago

mhkc commented 5 months ago

This PR fix a bug that prevented sourmash clustering introduced by the new dynamic sample id assignment.

The sample ids are now encoded as signature names when a new signature is written to disk.

Close #167

How to setup and perform the tests

Checkout repo and setup new Bonsai dev instance
Upload a test sample to bonsai, BONSAI_USER=admin BONSAI_PASSWD=admin ./upload_sample.py --api http://mtlucmds2.lund.skane.se:8811 -i ./test_sample.yml
Verify that the sourmash signatures were saved in the minhash_service logs
To to the uploaded sample and see if the clustering works

Expected outcome

Finding similar samples and the dendrogram in the samples view should work.