alfonsoguv/deepdna-mcp

Started the README's local MCP server (uvx [email protected]) over stdio and listed its tools via initialize + tools/list; server reported name deepdna-local 0.1.1 and tools read_dna_file and lookup_drug_gene (among others).

cd <host-path> && ls -la && cat README.md 2>/dev/null | head -300
cd <host-path> && git log -1 --format=%H 2>/dev/null; ls .github/workflows 2>/dev/null; cat pyproject.toml package.json 2>/dev/null | head -80
which uv uvx pip3 python3; python3 --version; python3 -m venv --help >/dev/null 2>&1 && echo venv_ok; cat <host-path>; ls <host-path> 2>/dev/null; echo "CDP=$CDP_URL"
curl -LsSf https://astral.sh/uv/install.sh | env UV_INSTALL_DIR=/usr/local/bin sh 2>&1 | tail -5; which uv uvx; uv --version
curl -LsSf https://astral.sh/uv/install.sh | sudo env UV_INSTALL_DIR=/usr/local/bin sh 2>&1 | tail -3; which uv uvx && uv --version
cd /tmp && export NODE_USE_ENV_PROXY=1 && { printf '%s\n' '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2025-06-18","capabilities":{},"clientInfo":{"name":"smoke","version":"0"}}}' '{"jsonrpc":"2.0","method":"notifications/initialized"}' '{"jsonrpc":"2.0","id":2,"method":"tools/list"}'; sleep 20; } | timeout 120 uvx [email protected] 2>/tmp/uvx_err.txt | head -c 4000; echo "rc=${PIPESTATUS[1]}"; tail -5 /tmp/uvx_err.txt
cd <host-path> && mkdir -p .coldpass && ls -la .coldpass && cat > .coldpass/probe.json <<'EOF'
{"kind":"mcp","argv":["/usr/local/bin/uvx","[email protected]"],"cwd":"/tmp"}
EOF
cat > .coldpass/report.json <<'EOF'
{"outcome":"working","operation":"Started the README's local MCP server (uvx [email protected]) over stdio and listed its tools via initialize + tools/list; server reported name deepdna-local 0.1.1 and tools read_dna_file and lookup_drug_gene (among others).","operation_scope":"Verified start and tools/list only. No DNA file was read and no lookup_drug_gene call was made, so the network-backed lookup against deepdna.ai was not exercised. The remote hosted server (https://deepdna.ai/mcp) was not tested.","steps":["Read README.md","Checked python3 3.12.3 present, no uv installed","Installed uv 0.13.1 via README-style installer: curl -LsSf https://astral.sh/uv/install.sh | sh (UV_INSTALL_DIR=/usr/local/bin)","Ran README command: uvx [email protected] as stdio MCP server; sent initialize, notifications/initialized, tools/list"],"deviations":["uv installer failed as non-root writing to /usr/local/bin; re-ran with sudo env UV_INSTALL_DIR=/usr/local/bin and it succeeded","Probe uses absolute path /usr/local/bin/uvx because the checker runs in a clean process"],"stuck_step":null,"main_blocker":null,"suggested_fix":null}
EOF
<env-var>=<host-path> python3 -I <host-path> --validate; echo rc=$?
pgrep -af deepdna || echo "no leftover deepdna processes"