Improve local dev setup for clinvar-vrsification

[larrybabb]

Summary

• Add HGVS_SEQREPO_DIR and fake AWS credentials to clinvar-vrsification script to prevent slow NCBI eutils fallback (~30x speedup) and boto3 using real ~/.aws/credentials against the local DynamoDB endpoint
• Document all required env vars in the script header and README
• Fix variation-normalizer-compose.yaml to use ${SEQREPO_ROOT_DIR}/.. instead of a hardcoded developer path
• Refactor main.py __main__ to only require UTA_DB_URL when --liftover is set
• Pin agct and cool-seq-tool transitive dependencies in pyproject.toml
• Add buckets/ to .gitignore

Test plan

• Set required env vars from README and run misc/clinvar-vrsification <release_date>
• Verify services start with podman-compose -f variation-normalizer-compose.yaml up -d
• Confirm no NCBI eutils calls in the log output
• Confirm script runs without UTA_DB_URL set when --liftover is not passed

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR improves the local development experience for running “ClinVar VRS-ification” and related services by standardizing environment configuration, speeding up sequence resolution by forcing local SeqRepo usage, and making liftover-related dependencies optional unless requested.

Changes:

• Updated local compose setup to mount SeqRepo from a configurable host path instead of a developer-specific hardcoded path.
• Documented/added required environment variables (including HGVS_SEQREPO_DIR and dummy AWS credentials) to avoid slow network fallbacks and unintended AWS credential usage.
• Adjusted __main__ startup checks so UTA_DB_URL is only required when --liftover is enabled; added dependency pins and ignored local output buckets.

Reviewed changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
variation-normalizer-compose.yaml	Replaces a hardcoded SeqRepo host path with a variable-based mount for local dev.
README.md	Documents HGVS_SEQREPO_DIR to ensure hgvs uses local SeqRepo instead of NCBI eutils.
pyproject.toml	Adds dependency pins to stabilize transitive dependency resolution.
misc/clinvar-vrsification	Documents required env vars and sets dummy AWS credentials for local runs.
clinvar_gk_pilot/main.py	Makes UTA_DB_URL required only when --liftover is set.
.gitignore	Ignores generated buckets/ output directory.

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