New HPO release 2024-08-13

[northwestwitch]

Perfect timing for the new Scout release, so we can update the database after release and deploying scout next week!

Link to the new release ---> https://github.com/obophenotype/human-phenotype-ontology/releases/tag/v2024-08-13

[northwestwitch]

Ok testing the database updates now:

Stage updates

Download files for updating

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml download everything --api-key blablabla

Update HPO terms

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update hpo --hpoterms hpo.obo --hpo-to-genes phenotype_to_genes.txt

Updating diseases

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update diseases -f .

Updating genes

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update genes -f .

Update the OMIM AUTO panel

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update omim --institute cust002 --genemap2 genemap2.txt --mim2genes mim2genes.txt

Update the PanelApp green genes panel

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update panelapp-green -i cust002 --force

[northwestwitch]

See the latest test above: it gets an error and I've opened the following issue to address it

[northwestwitch]

Prod updates

Update HPO terms

scout update hpo --hpoterms hpo.obo --hpo-to-genes phenotype_to_genes.txt

Updating diseases

scout update diseases -f .

Updating genes

scout update genes -f .

Update the OMIM-AUTO panel

scout update omim --institute cust002 --genemap2 genemap2.txt --mim2genes mim2genes.txt

Update the PanelApp green genes panel

scout update panelapp-green -i cust002 --force