Adding gfaidx backend support for indexed genome graph queries - #136

Merged

milot-mirdita merged 8 commits into

soedinglab:masterfrom

fawaz-dabbaghieh:graphviz

Sep 13, 2026

Commits on Sep 4, 2026

adding some notes on how to install locally and run on mac
fawaz-dabbaghieh
committed
623c617

Commits on Sep 7, 2026

gfaidx first implementation, Queued gfaidx job type and deterministic ticket ID, HTTP endpoints in backend/gfaidxapi.go, Tests covering validation, command construction, submission, polling, and re…
fawaz-dabbaghieh
committed
659c4a5
ability to list available graphs, ability to list the available paths and coordinates for a graph, parse the region paths tsv and return a JSON with this information, add discovery, parsing, and co…
fawaz-dabbaghieh
committed
35f5866

Commits on Sep 9, 2026

adding gfaidx to docker, now inside docker, it builds gfaidx from the source code in the gfaidx repository, because gfaidx doesn't really use much dependencies, it should be easy and straightforwar…
fawaz-dabbaghieh
committed
c7670bd

Commits on Sep 10, 2026

made some of the changes that milot pointed out in his comments, for the problem with Foldseek Interface, I just change the docker config to point to foldseek binary, I wasn't sure how to remove it…
fawaz-dabbaghieh
committed
e43ebee

Commits on Sep 11, 2026

Commits on Sep 13, 2026

removing the exposure of the threads to the user, now runs by default with 1 thread, and can be configured on the server deployment side or docker side, but not by user API requests
fawaz-dabbaghieh
committed
8a1bbc0