# Configuration Examples
This document provides practical examples of configuring the Enrichr MCP Server for different research scenarios and use cases.
## Quick Start Configurations
### 1. GO Biological Process Only (Your Current Need)
Perfect for users who only want GO Biological Process enrichment:
```json
{
"mcpServers": {
"enrichr-go-bp": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "--libraries", "GO_Biological_Process_2025"]
}
}
}
```
**Benefits:**
- Simple, focused analysis
- Faster queries (single library)
- Clean, targeted results
**Usage:** After this configuration, all your `enrichr_analysis` tool calls will default to GO Biological Process 2025 unless you specify otherwise.
### 2. GO Trinity (All GO Categories)
For comprehensive Gene Ontology analysis:
```json
{
"mcpServers": {
"enrichr-go-full": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "-l", "GO_Biological_Process_2025,GO_Molecular_Function_2025,GO_Cellular_Component_2025"]
}
}
}
```
### 3. Pathways Focus
For pathway-centric research:
```json
{
"mcpServers": {
"enrichr-pathways": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "--libraries", "KEGG_2021_Human,Reactome_2022,WikiPathways_2023_Human,MSigDB_Hallmark_2020"]
}
}
}
```
## Research-Specific Configurations
### Cancer Research Setup
```json
{
"mcpServers": {
"enrichr-cancer": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "-l", "GO_Biological_Process_2025,MSigDB_Hallmark_2020,KEGG_2021_Human,Human_Phenotype_Ontology,L1000_Kinase_and_GPCR_Perturbations_up"],
"env": {
"ENRICHR_SERVER_NAME": "cancer-enrichr"
}
}
}
}
```
### Neuroscience Research Setup
```json
{
"mcpServers": {
"enrichr-neuro": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server"],
"env": {
"ENRICHR_DEFAULT_LIBRARIES": "GO_Biological_Process_2025,Human_Phenotype_Ontology,GTEx_Tissue_Sample_Gene_Expression_Profiles_up,OMIM_Disease,ChEA_2022",
"ENRICHR_SERVER_NAME": "neuro-enrichr"
}
}
}
}
```
### Drug Discovery Setup
```json
{
"mcpServers": {
"enrichr-drug": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "--libraries", "DrugMatrix,L1000_Kinase_and_GPCR_Perturbations_up,KEGG_2021_Human,Human_Phenotype_Ontology,ChEA_2022"]
}
}
}
```
## Multi-Instance Configurations
You can run multiple instances with different default libraries:
```json
{
"mcpServers": {
"enrichr-go": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "-l", "GO_Biological_Process_2025", "-n", "go-enrichr"]
},
"enrichr-pathways": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "-l", "KEGG_2021_Human,Reactome_2022", "-n", "pathway-enrichr"]
},
"enrichr-disease": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "-l", "Human_Phenotype_Ontology,OMIM_Disease", "-n", "disease-enrichr"]
}
}
}
```
## Environment Variable Configurations
### Using .env File
Create a `.env` file in your project:
```bash
ENRICHR_DEFAULT_LIBRARIES=GO_Biological_Process_2025,KEGG_2021_Human
ENRICHR_SERVER_NAME=my-enrichr-server
```
Then in your MCP configuration:
```json
{
"mcpServers": {
"enrichr-server": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server"]
}
}
}
```
### System Environment Variables
```bash
# Set system-wide defaults
export ENRICHR_DEFAULT_LIBRARIES="GO_Biological_Process_2025"
export ENRICHR_SERVER_NAME="system-enrichr"
# Then use simple configuration
```
## Advanced Configurations
### Development vs Production
#### Development (comprehensive analysis)
```json
{
"mcpServers": {
"enrichr-dev": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "-l", "GO_Biological_Process_2025,KEGG_2021_Human,MSigDB_Hallmark_2020,Human_Phenotype_Ontology"]
}
}
}
```
#### Production (focused, fast)
```json
{
"mcpServers": {
"enrichr-prod": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "-l", "GO_Biological_Process_2025"]
}
}
}
```
### Lab-Specific Configurations
#### Immunology Lab
```json
{
"mcpServers": {
"enrichr-immuno": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "--libraries", "GO_Biological_Process_2025,KEGG_2021_Human,Reactome_2022,MSigDB_Hallmark_2020,GTEx_Tissue_Sample_Gene_Expression_Profiles_up"]
}
}
}
```
#### Metabolomics Lab
```json
{
"mcpServers": {
"enrichr-metab": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "-l", "GO_Biological_Process_2025,GO_Molecular_Function_2025,KEGG_2021_Human,Reactome_2022,HumanCyc_2016"]
}
}
}
```
## Testing Your Configuration
After setting up your configuration, test it:
1. **Restart your MCP client** (e.g., restart Cursor)
2. **Check server startup**: Look for startup messages showing your default libraries
3. **Test with simple gene list**:
```json
{
"name": "enrichr_analysis",
"arguments": {
"genes": ["TP53", "MYC", "EGFR"]
}
}
```
The tool should use your configured default libraries without needing to specify them.
## Troubleshooting Configuration
### Common Issues
1. **Libraries not recognized**: Check spelling and case sensitivity
2. **Comma separation**: Ensure no spaces after commas in CLI arguments
3. **JSON syntax**: Validate your JSON configuration
4. **Server not starting**: Check the server logs for error messages
### Validation
```bash
# Test your configuration locally
npx enrichr-mcp-server --libraries "GO_Biological_Process_2025" --help
```
### Getting Available Libraries
You can check available libraries at: https://maayanlab.cloud/Enrichr/#libraries
## Best Practices
1. **Start Simple**: Begin with 1-2 libraries, add more as needed
2. **Use Descriptive Names**: Name your servers based on their purpose
3. **Document Your Setup**: Keep notes on why you chose specific libraries
4. **Test Changes**: Always test configuration changes with known gene lists
5. **Version Control**: Keep your MCP configuration in version control
