Update documentation and add setup files#33
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Significantly expand README with UTA troubleshooting, port conflict guidance, dummy AWS credentials documentation, and release processing script usage. Add uta-setup.sql required by the compose file and CLAUDE.md for AI-assisted development. Fix SeqRepo volume mount path in compose file. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Pull request overview
This PR updates local setup documentation and supporting files for running the required UTA/Gene Normalizer services via Docker Compose, including adding a UTA initialization SQL script and AI-assistant context.
Changes:
- Updates
README.mdwith UTA troubleshooting steps (download gate/manual restore), port conflict guidance, dummy AWS credentials, and a release-processing script note. - Adds
uta-setup.sqlreferenced by the compose file for UTA DB initialization. - Updates compose SeqRepo mount guidance, adds
CLAUDE.md, and extends.gitignore.
Reviewed changes
Copilot reviewed 4 out of 5 changed files in this pull request and generated 10 comments.
Show a summary per file
| File | Description |
|---|---|
| variation-normalizer-compose.yaml | Updates SeqRepo mount guidance/path for the compose-based services setup. |
| uta-setup.sql | Adds a SQL init script intended to run during UTA container initialization. |
| README.md | Expands setup/troubleshooting docs, env var guidance, and release script usage. |
| CLAUDE.md | Adds AI-assisted development context and repository usage notes. |
| .gitignore | Ignores buckets cache directory, uv lockfile, and local Claude settings. |
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| volumes: | ||
| - uta_vol:/var/lib/postgresql/data | ||
| # - /usr/local/share/seqrepo:/usr/local/share/seqrepo | ||
| - /Users/kferrite/dev/data/seqrepo:/usr/local/share/seqrepo:ro | ||
| # Update this path to your local SeqRepo installation | ||
| - /usr/local/share/seqrepo:/usr/local/share/seqrepo:ro |
| export AWS_DEFAULT_REGION=us-east-2 | ||
| ``` | ||
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| **Important**: If you modified the ports in the compose file, update the corresponding environment variables accordingly (e.g., change `5432` to `5433` in `UTA_DB_URL` if you changed the UTA port). |
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| ### Parallelism | ||
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| Parallelism is configurable and uses python multiprocessing and multiprocessing queues. Some parallelism is significantly beneficial but since there is interprocess communication overhead and they are hitting the same filesystem there can be diminishing returns. On a Macbook Pro with 16 cores, setting parallelism to 4-6 provides clear benefit, but exceeding 10 saturates the machine and may be counterproductive. The code will partition the input file into `<parallelism>` number of files and each worker will process one, and then the outputs will be combined. |
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| \c uta; | |||
| GRANT CONNECT ON DATABASE uta TO anonymous; | ||
| GRANT SELECT, INSERT, UPDATE, DELETE ON ALL TABLES IN SCHEMA uta_20241220 TO anonymous; | ||
| ALTER DATABASE uta OWNER TO anonymous; | ||
| ALTER SCHEMA uta_20241220 OWNER to anonymous; |
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| # Copy into the container and restore | ||
| docker cp /tmp/uta_20241220.pgd.gz <uta_container_name>:/tmp/uta_20241220.pgd.gz | ||
| docker exec <uta_container_name> bash -c \ | ||
| 'gzip -cdq /tmp/uta_20241220.pgd.gz | psql -1e -U uta_admin -d uta -v ON_ERROR_STOP=1' |
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| # Database URLs (from Docker compose services) | ||
| export UTA_DB_URL=postgresql://anonymous:anonymous@localhost:5432/uta/uta_20241220 | ||
| export GENE_NORM_DB_URL=http://localhost:8000 |
| ## External Dependencies | ||
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| ### Required Services | ||
| The project requires these Docker services from variation-normalization: |
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| curl -o variation-normalizer-compose.yaml https://raw.githubusercontent.com/cancervariants/variation-normalization/0.15.0/compose.yaml | ||
| docker compose -f variation-normalizer-compose.yaml up -d |
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| - UTA database (port 5432): Universal Transcript Archive | ||
| - Gene Normalizer database (port 8000): Gene normalization service | ||
| - Variation Normalizer API (port 8001): Variation normalization service |
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Summary
uta-setup.sqlrequired by the compose file for UTA database initializationCLAUDE.mdfor AI-assisted development contextbuckets/,uv.lock, and.claude/settings.local.jsonto.gitignoreTest plan
docker compose -f variation-normalizer-compose.yaml up -dstill works with the updated compose file🤖 Generated with Claude Code