Setting Up Papergraph
lotchuazzz-crypto/papergraph-mcp
A skill your agent uses when a user has cloned PaperGraph MCP and asks to install, initialize, configure, set up, or start using it with an agent or MCP client.
File a bug or feature request against this MCP server's own repo.
$ npx skills add cyanheads/pubmed-mcp-server --skill report-issue-local -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install cyanheads/pubmed-mcp-server report-issue-local --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/cyanheads/pubmed-mcp-server.git skills-src && mkdir -p .claude/skills && cp -r skills-src/framework-skills/report-issue-local .claude/skills/report-issue-local && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "report-issue-local" agent skill from https://github.com/cyanheads/pubmed-mcp-server/tree/main/framework-skills/report-issue-local into .claude/skills/report-issue-local/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "report-issue-local", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/cyanheads/pubmed-mcp-server/tree/main/framework-skills/report-issue-localType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add cyanheads/pubmed-mcp-server --skill report-issue-local -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install cyanheads/pubmed-mcp-server report-issue-local --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/cyanheads/pubmed-mcp-server.git skills-src && mkdir -p .agents/skills && cp -r skills-src/framework-skills/report-issue-local .agents/skills/report-issue-local && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "report-issue-local" agent skill from https://github.com/cyanheads/pubmed-mcp-server/tree/main/framework-skills/report-issue-local into .agents/skills/report-issue-local/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "report-issue-local", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add cyanheads/pubmed-mcp-server --skill report-issue-local -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install cyanheads/pubmed-mcp-server report-issue-local --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/cyanheads/pubmed-mcp-server.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/framework-skills/report-issue-local .cursor/skills/report-issue-local && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "report-issue-local" agent skill from https://github.com/cyanheads/pubmed-mcp-server/tree/main/framework-skills/report-issue-local into .cursor/skills/report-issue-local/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "report-issue-local", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/cyanheads/pubmed-mcp-server.git --path framework-skills/report-issue-local--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add cyanheads/pubmed-mcp-server --skill report-issue-local -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install cyanheads/pubmed-mcp-server report-issue-local --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/cyanheads/pubmed-mcp-server.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/framework-skills/report-issue-local .gemini/skills/report-issue-local && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "report-issue-local" agent skill from https://github.com/cyanheads/pubmed-mcp-server/tree/main/framework-skills/report-issue-local into .gemini/skills/report-issue-local/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "report-issue-local", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install cyanheads/pubmed-mcp-server report-issue-localInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add cyanheads/pubmed-mcp-server --skill report-issue-local -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/cyanheads/pubmed-mcp-server.git skills-src && mkdir -p .github/skills && cp -r skills-src/framework-skills/report-issue-local .github/skills/report-issue-local && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "report-issue-local" agent skill from https://github.com/cyanheads/pubmed-mcp-server/tree/main/framework-skills/report-issue-local into .github/skills/report-issue-local/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "report-issue-local", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add cyanheads/pubmed-mcp-server --skill report-issue-local -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install cyanheads/pubmed-mcp-server report-issue-local --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/cyanheads/pubmed-mcp-server.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/framework-skills/report-issue-local .opencode/skills/report-issue-local && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "report-issue-local" agent skill from https://github.com/cyanheads/pubmed-mcp-server/tree/main/framework-skills/report-issue-local into .opencode/skills/report-issue-local/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "report-issue-local", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
report-issue-localFile a bug or feature request against this MCP server's own repo.
Report Issue Local is an agent skill from cyanheads/pubmed-mcp-server. File a bug or feature request against this MCP server's own repo. Use for server-specific issues — tool logic, service integrations, config problems, or domain bugs that aren't caused by the framework.
Its SKILL.md is about 3.3k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Agent Workflows, covering MCP servers. It works with Model Context Protocol. The repository describes itself as: Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP. The licence is Apache-2.0.
4 steps, taken from the first numbered list in SKILL.md.
Read from SKILL.md and the folder at commit 5a417fb. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Shell commands in SKILL.md call:
ghbunFrom the folder's file list and the shell code blocks in SKILL.md.
Hosts in commands or code, which the agent is likely to contact:
hono.devsupabase.comgithub.comFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Report Issue Local loads about 3.3k tokens when it runs. Until then it costs about 55 tokens; SKILL.md has 1,215 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
The full file from cyanheads/pubmed-mcp-server at commit 5a417fb, republished under its Apache-2.0 licence (© cyanheads). 1,215 words, ~3,255 tokens.
.claude/skills/report-issue-local/SKILL.md (or your agent's skills folder).The bug is in this server's code, not in @cyanheads/mcp-ts-core. Typical triggers:
server-config.ts) rejects valid env vars or has wrong defaults.describe() on schema fields causing poor LLM tool useIf the issue is in the framework itself (builders, Context, utilities, type exports, linter), use report-issue-framework instead.
For general gh CLI workflows outside issue filing (PRs, workflows, API access), see the github-cli skill.
gh repo view --json nameWithOwner -q '.nameWithOwner'gh issue list --search "your error message or keyword" --state all
# Assess a close match before commenting — is it already linked to a fix or referenced elsewhere?
gh issue view <number> # body
gh issue view <number> --comments # thread only — without a TTY it prints no body
gh api 'repos/{owner}/{repo}/issues/<number>/timeline' --paginate \
--jq '.[] | select(.event=="cross-referenced") | .source.issue | "\(.repository.full_name)#\(.number) — \(.title)"'Reproduce the issue — confirm it's reproducible. Note the exact input, transport mode, and any relevant env vars.
Check logs — review ctx.log output and any framework telemetry for clues. If running HTTP, check the response body for structured error details.
Good issues are terse and fact-dense. Budget: a bug reads in ~150 words, a feature in ~250, code and logs excluded. Every section past the form's required fields must earn its place — a section you could delete without changing the fix is noise. One or two sentences per bullet; if a bullet runs long, split it or cut it.
search_docs returns an empty array for queries containing &" beats "Search is broken." A reader should know what's wrong before the end of the first sentence.[Hono](https://hono.dev/), [Supabase](https://supabase.com/). Link to the canonical repo or homepage so readers can verify the dependency and reach docs in one click.owner/repo#N for cross-repo issue references. GitHub auto-renders them as linked references (e.g. cyanheads/mcp-ts-core#46). Bare #N only works for same-repo issues — useful when the bug depends on or relates to a framework issue.Related: #N line near the top when the issue grows from prior context (discussions, other issues, PRs). Makes provenance clickable.Related:, the description, or Additional context — not all three. The reader sees them all; redundant linking dilutes signal.Depends on: owner/repo#N to declare ordering explicitly when implementation is blocked on an upstream framework change or another issue landing first.GitHub issues are public. Do not include secrets, credentials, API keys, or tokens. Redact sensitive values from env vars, headers, and logs before submitting. Replace with obvious placeholders: REDACTED, sk-...REDACTED. Do not rely on partial masking — partial keys can still be exploited.
This repo includes YAML form issue templates (scaffolded from the framework). Use --web to open the form in the browser (preferred when available), or pass --title + --body for non-interactive use.
gh issue create --template "Bug Report" --webStructure the --body to match the template's form fields. Description is two or three sentences; the reproduction is the exact input and the observed output, nothing else. Add ### Additional context only when it changes the fix (a workaround, a related issue, the one log line that matters) — omitted by default.
gh issue create \
--title "bug(tool_name): concise description" \
--label "bug" \
--assignee "@me" \
--body "$(cat <<'ISSUE'
### Server version
<package.json version>
### mcp-ts-core version
<installed version from node_modules/@cyanheads/mcp-ts-core/package.json — not the ^ range>
### Runtime
Bun
### Runtime version
<bun --version>
### Transport
stdio
### Description
What happened and what you expected instead.
### Steps to reproduce
1. Call `tool_name` with input: `{ "key": "value" }`
2. Observe error / wrong output
### Actual behavior
```
Error or incorrect output here
```
### Expected behavior
What should have happened.
ISSUE
)"Format: type(scope): description
bug, feat, docs, choreconfig, auth, or domain areaExamples:
bug(search_docs): returns empty results for queries with special charactersfeat(analytics): add date range filter to usage_report tooldocs(setup): .env.example missing REDIS_URLEvery issue needs exactly one primary label. Stack secondary labels on top when applicable.
Primary (required — pick one):
| Label | When |
|---|---|
bug | Something broken |
enhancement | New feature or improvement |
documentation | Documentation is wrong, missing, or misleading |
Secondary (optional — stack on top of primary):
| Label | When |
|---|---|
regression | Worked before, broken after a change |
performance | Memory, CPU, latency, or resource usage |
security | Vulnerability, CVE, or hardening work |
breaking-change | Change will break public API or an existing tool contract |
blocked-by-framework | Fix requires a released change in @cyanheads/mcp-ts-core; pairs with a Depends on: cyanheads/mcp-ts-core#N line in the body |
blocked-by-sdk | Fix requires changes in @modelcontextprotocol/sdk |
surplus-token-idea | Worth exploring when token budget allows |
blocked-by-framework comes off when this server adopts the release that ships the fix. An issue blocked on the SDK through the framework takes blocked-by-framework, not blocked-by-sdk — the server's own unblock is still a framework release.
Combine labels: --label "bug" --label "regression".
Secondary labels are not GitHub defaults — if gh issue create --label "regression" fails with label not found, create it once:
gh label create regression --color e99695 --description "Worked before, broken after a change"
gh label create performance --color 5319e7 --description "Memory, CPU, latency, or resource usage"
gh label create security --color b60205 --description "Vulnerability, CVE, or hardening work"
gh label create breaking-change --color d93f0b --description "Change will break public API or an existing tool contract"
gh label create blocked-by-framework --color fbca04 --description "Fix requires a released change in @cyanheads/mcp-ts-core"
gh label create blocked-by-sdk --color c5def5 --description "Fix requires changes in @modelcontextprotocol/sdk"
gh label create surplus-token-idea --color FF10F0 --description "Worth exploring when token budget allows"Note: --body-file replaces the entire body — it does not supplement a --body flag. For structured bugs with logs, either embed the log content in the Additional context section of a normal --body, or file the issue first and add the log as a comment:
bun run rebuild && bun run start:stdio 2>&1 | head -200 > /tmp/server-error.log
# As part of a new issue (the log becomes the entire body — no template fields)
gh issue create \
--title "bug(ingest): crashes on large payload" \
--label "bug" \
--assignee "@me" \
--body-file /tmp/server-error.log
# Or as a comment on an existing issue (preferred — keeps the structured body intact)
gh issue comment <number> --body-file /tmp/server-error.loggh issue create --template "Feature Request" --webThe first three headings are the Feature Request form's own fields, in its order — Use case and Proposed behavior are required by the form, so a body without them does not satisfy it. Out of scope is one or two lines. Nothing else by default: a Scope, Flow, Design / Tradeoffs, or Depends on block is added only when the reader cannot act without it, and each stays to a few lines.
gh issue create \
--title "feat(scope): concise description" \
--label "enhancement" \
--assignee "@me" \
--body "$(cat <<'ISSUE'
### Use case
One or two sentences: who hits this gap and why it matters. Name the specific tool, service, resource, or domain area. Kept short on purpose — a field that invites a paragraph gets padded with background and skipped by the next reader.
Related: #N
### Proposed behavior
What you want the server to do, then the new behavior or surface. For tool/resource changes, show example input/output or the new schema fields. Link external libraries or services on first mention: [lib name](https://github.com/owner/repo).
```ts
// Example: new input field or output shape
```
### Alternatives considered
What you tried or evaluated instead, and why it didn't fit.
### Out of scope
- Adjacent work that belongs in a separate issue
ISSUE
)"Not sure where the bug lives? Quick checks:
| Signal | Likely framework | Likely server |
|---|---|---|
Error originates in node_modules/@cyanheads/mcp-ts-core/ | Yes | |
Error in src/mcp-server/tools/ or src/services/ | Yes | |
Same bug reproduces with a bare tool() definition (no services) | Yes | |
| Bug disappears when you swap in a dummy handler | Yes | |
ctx.state, ctx.log, ctx.inputs behave wrong on any tool | Yes | |
| Only one specific tool/resource is affected | Yes |
When genuinely ambiguous, file against this server's repo and note that it might be a framework issue. The maintainer can transfer it upstream.
# View the issue body, then its comment thread (--comments without a TTY prints no body)
gh issue view <number>
gh issue view <number> --comments
# Add context
gh issue comment <number> --body "Additional findings..."
# List your open issues
gh issue list --author @me
# Close if resolved
gh issue close <number> --reason completed --comment "Fixed in <commit or PR>"type(scope): description formatbug / enhancement / documentation)Use case and Proposed behavior present (the form's required fields), Alternatives considered third; Out of scope defined© cyanheads, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Just SKILL.md in framework-skills/report-issue-local of cyanheads/pubmed-mcp-server.
Open the folder on GitHubat commit 5a417fb
Report Issue Local next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Report Issue Local this skillcyanheads/pubmed-mcp-server | 156 | — | ~3.3k | Automated safety check: Pass | Apache-2.0 | |
| Setting Up Papergraphlotchuazzz-crypto/papergraph-mcp | 285 | — | ~3.3k | Automated safety check: Pass | MIT | |
| Just PRs MCPClawBio/ClawBio | 1.2k | — | ~3.5k | Automated safety check: Pass | MIT | |
| Patsnap Current Awarenesspatsnap/mcp | 113 | — | ~671 | Automated safety check: Pass | Apache-2.0 | |
| Patsnap Scientific Translational Evidencepatsnap/mcp | 113 | — | ~728 | Automated safety check: Pass | Apache-2.0 | |
| Peer Review Loophashgraph-online/awesome-codex-plugins | 1.3k | — | ~2.3k | Automated safety check: Pass | Apache-2.0 |
lotchuazzz-crypto/papergraph-mcp
A skill your agent uses when a user has cloned PaperGraph MCP and asks to install, initialize, configure, set up, or start using it with an agent or MCP client.
ClawBio/ClawBio
Compute evidence-aware polygenic risk scores from a local VCF or WGS file through the validated just-prs engine and a pinned local just-prs MCP server.
patsnap/mcp
Patsnap Current Awareness MCP for AI agents. An agent skill from patsnap/mcp.
patsnap/mcp
Patsnap Scientific & Translational Evidence MCP for AI agents.
hashgraph-online/awesome-codex-plugins
Peer Review Ralph Loop — combines Cavekit kits with a Ralph Loop and true cross-model peer review using Codex (OpenAI).
anthropics/skills
Guides the design and implementation of Model Context Protocol servers in TypeScript or Python, from tool naming and error messages to evaluation.
cyanheads/pubmed-mcp-server
Scaffold an MCP App tool + UI resource pair. An agent skill from cyanheads/pubmed-mcp-server.
cyanheads/pubmed-mcp-server
Scaffold a new MCP prompt template. An agent skill from cyanheads/pubmed-mcp-server.
cyanheads/pubmed-mcp-server
Scaffold a new MCP resource definition. An agent skill from cyanheads/pubmed-mcp-server.
cyanheads/pubmed-mcp-server
Scaffold a new service integration. An agent skill from cyanheads/pubmed-mcp-server.
cyanheads/pubmed-mcp-server
Scaffold a test file for an existing tool, resource, or service.
cyanheads/pubmed-mcp-server
Authentication, authorization, and multi-tenancy patterns for @cyanheads/mcp-ts-core.
Works with
Categories
File a bug or feature request against this MCP server's own repo. Report Issue Local is an agent skill from cyanheads/pubmed-mcp-server. File a bug or feature request against this MCP server's own repo.
Report Issue Local fits situations like: server-specific issues — tool logic; service integrations; config problems; domain bugs that arent caused by the framework.
Run `npx skills add cyanheads/pubmed-mcp-server --skill report-issue-local -a claude-code`. Or copy the skill folder (framework-skills/report-issue-local in cyanheads/pubmed-mcp-server) into .claude/skills/report-issue-local in your project. Claude Code loads it when a task matches its description.
Run `npx skills add cyanheads/pubmed-mcp-server --skill report-issue-local -a codex`. Or copy the skill folder (framework-skills/report-issue-local in cyanheads/pubmed-mcp-server) into .agents/skills/report-issue-local in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add cyanheads/pubmed-mcp-server --skill report-issue-local -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/report-issue-local, .gemini/skills/report-issue-local, .github/skills/report-issue-local and .opencode/skills/report-issue-local in your project.
Going by SKILL.md and its folder, Report Issue Local needs the command-line tools its instructions call (gh and bun).
SKILL.md names 3 domains. In commands or code: hono.dev, supabase.com and github.com; the agent is likely to contact these when it follows the instructions. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
Report Issue Local is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 3.3k tokens (SKILL.md is roughly 13k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Report Issue Local: Setting Up Papergraph (lotchuazzz-crypto/papergraph-mcp, 285 stars), Just PRs MCP (ClawBio/ClawBio, 1.2k stars), Patsnap Current Awareness (patsnap/mcp, 113 stars) and Patsnap Scientific Translational Evidence (patsnap/mcp, 113 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
cyanheads (a GitHub user) maintains it in cyanheads/pubmed-mcp-server, which has 156 GitHub stars. The repository holds 30 skills in this directory. The repository was last updated on October 4, 2026.
Source: cyanheads/pubmed-mcp-server on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.