docs: add Docker MCP Toolkit + SQLite MCP runbook#620
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Adds docs/docker-mcp-sqlite.md, a reproducible recipe for installing the SQLite MCP server into Docker MCP Toolkit so any connected MCP client (Claude Code, Cursor, VS Code, etc.) gains six SQLite tools alongside graphify's knowledge-graph tools. Notes the catalog has two SQLite images at time of writing: `mcp/sqlite` (marked Archived but works) and `mcp/sqlite-mcp-server` (broken entrypoint). Recommends the working one. Linked from README.md under a new 'Optional integrations' section. This is unrelated to the upstream graphify pipeline; it lives as an optional companion runbook for users who want a lightweight persistent SQL workspace exposed to their MCP-aware AI clients. Co-Authored-By: Oz <oz-agent@warp.dev>
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Pull request overview
Adds an optional documentation runbook describing how to set up the Docker MCP Toolkit with a SQLite MCP server, and links it from the main README so users can discover it without impacting graphify’s core pipeline/docs.
Changes:
- Added a new runbook:
docs/docker-mcp-sqlite.mdcovering install, smoke tests, persistence, client wiring, uninstall, and troubleshooting. - Linked the new runbook from
README.mdunder a new “Optional integrations” section.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| docs/docker-mcp-sqlite.md | New end-to-end setup/runbook for Docker MCP Toolkit + SQLite MCP server, including troubleshooting and persistence notes. |
| README.md | Adds an “Optional integrations” section with a link to the new runbook. |
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| docker mcp tools call read_query \ | ||
| query='SELECT * FROM notes ORDER BY id' | ||
| docker mcp tools call describe_table table_name=notes | ||
| docker mcp tools call append_insight insight='3 rows inserted; aggregates work.' |
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The example append_insight text says "3 rows inserted" but the preceding INSERT statement inserts 2 rows. This makes the smoke test internally inconsistent; update the insight text or the insert statement so they match.
Suggested change
| docker mcp tools call append_insight insight='3 rows inserted; aggregates work.' | |
| docker mcp tools call append_insight insight='2 rows inserted; aggregates work.' |
| The Docker MCP gateway should now expose 6 additional tools: | ||
| ```bash | ||
| docker mcp tools count | ||
| # → 15 tools (was 9 before adding SQLite) |
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docker mcp tools count output is installation/profile dependent; hard-coding "15 tools (was 9)" may be incorrect for users with other servers enabled or different Docker versions. Consider stating that the count should increase by 6 after adding SQLite, or show how to list tool names instead of relying on a specific total.
Suggested change
| # → 15 tools (was 9 before adding SQLite) | |
| # The total is installation/profile dependent; it should be 6 higher than before adding SQLite. |
This was referenced Apr 30, 2026
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Adds docs/colabfold-macos-install.md, a reproducible recipe for installing LocalColabFold (ColabFold + AlphaFold2 weights) on Apple Silicon Macs, so users can predict protein structures locally and feed the resulting PDBs / confidence scores into a graphify corpus. Notes upstream LocalColabFold's current top-level installer hardcodes Linux x86_64 Miniforge and jax[cuda12], which fail on Apple Silicon (no macOS CUDA wheels, no NVIDIA GPU). Recommends the bundled v1.5.5 M1 installer as the working Apple Silicon path. ColabFold 1.6.1 with JAX 0.4.23 CPU build, verified by 60s smoke test on a 62-residue FASTA. Linked from README.md under the existing 'Optional integrations' section (also added by this PR if not already present from #620). Co-Authored-By: Oz <oz-agent@warp.dev>
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Summary
Adds
docs/docker-mcp-sqlite.md, a reproducible runbook for installing the SQLite MCP server into Docker MCP Toolkit. Once installed, any connected MCP client (Claude Code, Cursor, VS Code, etc.) gains six SQLite tools —read_query,write_query,create_table,list_tables,describe_table,append_insight— alongside graphify's knowledge-graph tools.The doc is optional and unrelated to graphify's pipeline. Linked from
README.mdunder a new "Optional integrations" section so it's discoverable without cluttering the main docs.Why
Many graphify users already run Docker Desktop and use AI clients with MCP. Pairing a lightweight, persistent SQL workspace with the knowledge graph is a natural fit and a common request.
Notes for reviewers
mcp/sqlite-mcp-serverhas a broken entrypoint (/app/.venv/bin/mcp-server-sqlitedoes not exist in the published layer);mcp/sqlite(marked "Archived" but functional) is recommended. The doc explains both and points at the working one.docker mcp profile server add→ all 6 tools callable viadocker mcp tools call→ data persists across container invocations on themcp-sqlitenamed volume.upstream/v5; does not include Fix invalid escape sequence SyntaxWarning in __main__.py #602's escape-sequence fix and does not conflict with it.Files
docs/docker-mcp-sqlite.md(new, ~140 lines)README.md(small "Optional integrations" section + table row)Co-Authored-By: Oz oz-agent@warp.dev