/CLI Reference

This is the complete reference for Celline's command-line interface (CLI). It provides detailed explanations of all commands, options, and usage examples.

🎯 Basic Syntax

      celline [command] [options] [arguments]

Global Options

OptionDescription
--help, -hDisplay help
--versionDisplay version information

📋 Main Commands

🚀 Project Management

init - Project Initialization

      celline init [project_name]

Initialize a new Celline project.

Parameters:

  • project_name (optional): Project name

Examples:

      # Initialize project with current directory name
celline init

# Initialize project with specified name
celline init my-scrna-project

info - System Information Display

      celline info

Display Celline system information and available functions.

Examples:

      celline info

⚙️ Configuration Management

config - Configuration Management

      celline config [options]

Manage execution environment configuration.

Options:

  • --system {multithreading,PBS}: Set execution system
  • --nthread N: Set number of threads
  • --pbs-server SERVER: Set PBS server name

Examples:

      # Interactive configuration
celline config

# Configure multithreaded execution
celline config --system multithreading --nthread 4

# Configure PBS cluster execution
celline config --system PBS --pbs-server my-cluster

📚 Help System

list - Function List Display

      celline list

Display all available functions in table format.

help - Detailed Help

      celline help [function_name]

Parameters:

  • function_name (optional): Function name for detailed help display

Examples:

      # Display general help
celline help

# Display help for specific functions
celline help add
celline help preprocess

🔧 Function Execution

run - Function Execution

      celline run <function_name> [function_args] [options]

Execute the specified function.

Options:

  • --project-dir, -p DIR: Project directory (default: .)
  • --project-name, -n NAME: Project name (default: default)

Examples:

      # Basic function execution
celline run preprocess

# Function execution with arguments
celline run add GSE123456

# Execute with specified project
celline run preprocess --project-dir /path/to/project

🌐 Interactive Mode

interactive - Web Interface Launch

      celline interactive

Launch web-based interactive interface and API server.

api - Launch API Server Only

      celline api

Launch only the API server for testing purposes.

🔬 Analysis Functions

📊 Data Management

add - Sample Addition

      celline run add <sample_ids> [options]

Add new samples to the project.

Parameters:

  • sample_ids: Sample IDs to add (GSE, GSM, SRR, etc.)

Options:

  • --title, -t TITLE: Sample title
  • --from-file, -f FILE: Load sample IDs from file

Examples:

      # Add single sample
celline run add GSE123456

# Add multiple samples
celline run add GSM789012 GSM789013 --title "My samples"

# Add from file
celline run add --from-file samples.txt

# Add from CSV file (requires id, title columns)
celline run add --from-file samples.csv

download - Data Download

      celline run download [options]

Download sequencing data for added samples.

Options:

  • --nthread, -n N: Number of download threads (default: 1)
  • --force, -f: Force re-download of existing files

Examples:

      # Basic download
celline run download

# Parallel download
celline run download --nthread 4

# Force re-download
celline run download --force

🧮 Data Processing

count - Count Processing

      celline run count [options]

Generate expression counts from FASTQ files using Cell Ranger.

Examples:

      celline run count

create_seurat - Seurat Object Creation

      celline run create_seurat [options]

Create Seurat objects from count data.

Examples:

      celline run create_seurat

🔬 Quality Control & Preprocessing

preprocess - Preprocessing

      celline run preprocess [options]

Execute quality control, filtering, and normalization.

Options:

  • --target-celltype, -t TYPES: Specify target cell types (multiple allowed)

Examples:

      # Basic preprocessing
celline run preprocess

# Target specific cell types only
celline run preprocess --target-celltype Neuron Astrocyte

🔍 Analysis

reduce - Dimensionality Reduction

      celline run reduce [options]

Execute dimensionality reduction using PCA, UMAP, t-SNE.

predict_celltype - Cell Type Prediction

      celline run predict_celltype [options]

Predict cell types using machine learning models.

integrate - Data Integration

      celline run integrate [options]

Execute data integration and batch effect correction for multiple samples.

🗄️ Database Management

sync_DB - Database Synchronization

      celline run sync_DB [options]

Synchronize local database with the latest public databases.

set_transcriptome - Transcriptome Information Setting

      celline run set_transcriptome [options]

Configure transcriptome information database for analysis.

🎛️ Execution Environment Configuration

Multithreaded Execution

      # Execute in parallel with 4 threads
celline config --system multithreading --nthread 4

# Function execution
celline run download --nthread 4

PBS Cluster Execution

      # Configure PBS system
celline config --system PBS --pbs-server my-cluster

# Job submission
celline run count  # Executed as PBS job

📝 Configuration Files

setting.toml

      [project]
name = "my-project"
version = "1.0.0"

[execution]
system = "multithreading"  # or "PBS"
nthread = 4
pbs_server = "my-cluster"

[R]
r_path = "/usr/bin/R"

[fetch]
wait_time = 4

samples.toml

      # Sample information (auto-generated)
GSM1234567 = "Sample 1 description"
GSM1234568 = "Sample 2 description"

🔄 Workflow Examples

Basic Workflow

      #!/bin/bash
# Complete analysis workflow

# 1. Project initialization
celline init my-analysis

# 2. Configuration
celline config --system multithreading --nthread 4

# 3. Sample addition
celline run add GSE123456

# 4. Data processing
celline run download --nthread 4
celline run count
celline run create_seurat

# 5. Quality control & preprocessing
celline run preprocess

# 6. Analysis
celline run predict_celltype
celline run reduce
celline run integrate

# 7. Interactive analysis
celline interactive

Batch Processing

      # Bulk processing of multiple samples
echo "GSE123456\nGSE789012\nGSE345678" > datasets.txt

while read dataset; do
    echo "Processing $dataset"
    celline run add $dataset
    celline run download
    celline run count
    celline run preprocess
done < datasets.txt

🚨 Error Handling

Common Errors

      # When function is not found
celline run unknown_function
# Error: Function 'unknown_function' not found.

# When required arguments are missing
celline run add
# Error: Function name is required.

# When configuration error occurs
celline run download
# Error: No samples found. Use 'celline run add' first.

Log Checking

      # Check error logs
cat resources/*/log/*.log

# Real-time log monitoring
tail -f resources/*/log/*.log

🔧 Debugging and Troubleshooting

Getting Detailed Information

      # Display detailed system information
celline info

# Check configuration status
celline config

# Check available functions
celline list

Checking Execution Environment

      # Check Python environment
python -c "import celline; print(celline.__version__)"

# Check R environment
which R
R --version

For more detailed usage information, please refer to Configuration and Advanced Usage.