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Noctua MCP Server

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by geneontology
claude.yml3.32 kB
# Claude Code GitHub action # --- # This github action is from the copier template in https://github.com/ai4curation/github-ai-integrations, donated by the Monarch Initiative # For more documentation, see https://ai4curation.github.io/aidocs/how-tos/set-up-github-actions/ # Author: Chris Mungall (@cmungall) name: Claude Code on: issue_comment: types: [created] pull_request_review_comment: types: [created] issues: types: [opened, assigned] pull_request_review: types: [submitted] jobs: claude: if: | (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) || (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) || (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) || (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude'))) runs-on: ubuntu-latest permissions: contents: write pull-requests: write issues: write id-token: write actions: read # Required for Claude to read CI results on PRs steps: - name: Checkout repository uses: actions/checkout@v4 with: fetch-depth: 1 - name: Install uv uses: astral-sh/setup-uv@v5 - name: Install python tools run: | uv sync - name: Run Claude Code id: claude uses: anthropics/claude-code-action@beta with: claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }} mcp_config: | { "mcpServers": { "ols": { "command": "uvx", "args": [ "ols-mcp" ] }, "sequential-thinking": { "command": "npx", "args": [ "-y", "@modelcontextprotocol/server-sequential-thinking" ] } } } # This is an optional setting that allows Claude to read CI results on PRs additional_permissions: | actions: read # Optional: Specify model (defaults to Claude Sonnet 4, uncomment for Claude Opus 4.1) # model: "claude-opus-4-1-20250805" # Optional: Customize the trigger phrase (default: @claude) # trigger_phrase: "/claude" # Optional: Trigger when specific user is assigned to an issue # assignee_trigger: "claude-bot" # Optional: Allow Claude to run specific commands allowed_tools: "Bash(*),FileEdit,Edit,MultiEdit,WebSearch,WebFetch,mcp__ols_mcp__search_all_ontologies,mcp__ols_mcp__get_terms_from_ontology" # Optional: Add custom instructions for Claude to customize its behavior for your project # custom_instructions: | # Follow our coding standards # Ensure all new code has tests # Use TypeScript for new files # Optional: Custom environment variables for Claude # claude_env: | # NODE_ENV: test

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