feat: add Galaxy tool execution integration demo#894
Draft
dannon wants to merge 9 commits intogalaxyproject:mainfrom
Draft
feat: add Galaxy tool execution integration demo#894dannon wants to merge 9 commits intogalaxyproject:mainfrom
dannon wants to merge 9 commits intogalaxyproject:mainfrom
Conversation
Creates the base infrastructure layer for BRC Analytics backend: - FastAPI application with health and cache endpoints - Redis caching service with TTL management - Docker Compose setup (backend + redis + nginx) - nginx reverse proxy configuration - uv for dependency management - Ruff formatting for Python code - E2E health check tests This branch serves as the foundation for feature branches to build upon.
Adds GET /api/v1/version endpoint that returns: - API version (from APP_VERSION env var) - Environment (development/production) - Service name This provides a simple way for the frontend to display version info and demonstrates the backend infrastructure is working.
Use APP_VERSION build arg to inject version from package.json into backend container. Adds docker-build.sh script to automate this. All endpoints now use settings.APP_VERSION instead of hardcoded values.
builds on backend-infrastructure to add: - galaxy api integration via bioblend - job submission and monitoring capabilities - workflow execution - job history tracking - results retrieval - frontend galaxy ui (galaxyjob components, galaxyjobview) - react hooks for galaxy functionality - e2e test coverage for galaxy integration - galaxy configuration settings (api url, api key, tool ids) - bioblend dependency for galaxy communication this feature can be independently reviewed and tested
- Update README to describe Galaxy integration only (not LLM/ENA) - Sync .gitignore from infrastructure branch
dannon
changed the title
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Galaxy job submission and monitoring infrastructure. Requires the backend, currently just a demo random_lines tool, but this is where&how we will execute logansearch, lexicmap, etc., in the future for use from BRC without even visiting galaxy.
Summary
Depends on: #892