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Guide for setup arXiv MCP server via Docker MCP
1. Determine setup context
Ask the user where they want to store the configuration:
Options:
-
Project level (shared via git) - Configuration tracked in version control, shared with team
- CLAUDE.md updates go to:
./CLAUDE.md
-
Project level (personal preferences) - Configuration stays local, not tracked in git
- CLAUDE.md updates go to:
./CLAUDE.local.md
- Verify these files are listed in
.gitignore, add them if not
-
User level (global) - Configuration applies to all projects for this user
- CLAUDE.md updates go to:
~/.claude/CLAUDE.md
Store the user's choice and use the appropriate paths in subsequent steps.
2. Check if Docker MCP is available
First, verify that Docker MCP (MCP_DOCKER) is accessible by attempting to use mcp-find tool to search for servers.
If Docker MCP is NOT available:
- Ask user to install Docker Desktop following instructions at: https://docs.docker.com/desktop/
- After Docker Desktop is installed, guide user to connect MCP using: https://docs.docker.com/ai/mcp-catalog-and-toolkit/get-started/#claude-code
- Once configured, ask user to restart Claude Code and run "continue" to resume setup
3. Search and add paper-search MCP server
Write to user that regular arxiv-mcp-server is known to have issues, specifically is failing to initialize (EOF error during init). So we will use paper-search MCP server instead.
Use Docker MCP to find and add the paper-search MCP server which provides comprehensive academic paper search capabilities:
mcp-find query: "paper-search"
mcp-add name: "paper-search" activate: true
This server provides access to multiple academic sources:
- arXiv - preprints in physics, mathematics, computer science, etc.
- PubMed - biomedical literature
- bioRxiv/medRxiv - biology and medicine preprints
- Semantic Scholar - AI-powered research tool
- Google Scholar - broad academic search
- IACR - cryptography research
- CrossRef - DOI-based citation database
4. Test the setup
Verify the server is working by searching for papers:
mcp-exec name: "search_arxiv" arguments: {"query": "test query", "max_results": 2}
5. Update CLAUDE.md file
Use the path determined in step 1:
Once the paper-search MCP server is successfully set up, update CLAUDE.md file with the following content:
### Use Paper Search MCP for Academic Research
Paper Search MCP is available via Docker MCP for searching and downloading academic papers.
**Available tools**:
- `search_arxiv` - Search arXiv preprints (physics, math, CS, etc.)
- `search_pubmed` - Search PubMed biomedical literature
- `search_biorxiv` / `search_medrxiv` - Search biology/medicine preprints
- `search_semantic` - Search Semantic Scholar with year filters
- `search_google_scholar` - Broad academic search
- `search_iacr` - Search cryptography papers
- `search_crossref` - Search by DOI/citation
**Download and read tools**:
- `download_arxiv` / `read_arxiv_paper` - Download/read arXiv PDFs
- `download_biorxiv` / `read_biorxiv_paper` - Download/read bioRxiv PDFs
- `download_semantic` / `read_semantic_paper` - Download/read via Semantic Scholar
**Usage notes**:
- Use `mcp-exec` to call tools, e.g., `mcp-exec name: "search_arxiv" arguments: {"query": "topic", "max_results": 10}`
- Downloaded papers are saved to `./downloads` by default
- For Semantic Scholar, supports multiple ID formats: DOI, ARXIV, PMID, etc.
6. Alternative: arxiv-mcp-server
If you specifically need the dedicated arXiv MCP server with additional features (deep analysis prompts, local storage management), you can try:
mcp-find query: "arxiv"
mcp-config-set server: "arxiv-mcp-server" key: "storage_path" value: "/path/to/papers"
mcp-add name: "arxiv-mcp-server" activate: true
Note: This server requires configuration of a storage path for downloaded papers.
Weekly Installs
152
Repository
neolabhq/contex…ring-kit
GitHub Stars
699
First Seen
Feb 19, 2026
Installed on
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github-copilot145
codex145
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kimi-cli142
cursor142
