Add standalone FastAPI conservation server with CLI tools#191
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rdk wants to merge 2 commits intocusbg:mainfrom
Open
Add standalone FastAPI conservation server with CLI tools#191rdk wants to merge 2 commits intocusbg:mainfrom
rdk wants to merge 2 commits intocusbg:mainfrom
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- Conservation server exposing HMM pipeline via HTTP (port 8030) - run_conservation.py for single FASTA file processing - Batch script for parallel conservation computation - Input validation for HMM sequence database file - Docker Compose service and Dockerfile updates
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This is a request for comments, please don't merge yet.
See also https://github.com/rdk/prankweb/tree/conservation-server/executor-p2rank/conservation
Summary
/conservationendpoint) that exposes HMM-based conservation score computation over HTTP, decoupled from the full P2Rank prediction pipelinerun_conservation.py) for computing conservation on a single FASTA file and a batch processing wrapper (calculate_conservations_batch.sh) for parallel processing of FASTA directoriesconservation-serverservice todocker-compose.ymlwith documentation for building, running, and configuring the serverDetails
The conservation server wraps the existing HMM-based conservation pipeline (phmmer → esl-weight → esl-alistat) behind a simple HTTP API, allowing conservation scores to be computed without running a full P2Rank prediction. The
server reuses all existing conservation logic -- no computation code was duplicated.
The Docker setup extends the existing
executor-p2rankimage with FastAPI/uvicorn dependencies and can be run with multiple workers for concurrent requests.