Documentation

Comprehensive guides for using BioBuntu

CLI Reference

Complete command-line interface documentation

  • biobuntu --help
  • biobuntu create-project
  • biobuntu run
  • biobuntu validate
  • biobuntu list-projects

Web Dashboard

Web interface features and usage

  • Project management
  • Pipeline execution
  • Real-time monitoring
  • File download
  • Results visualization

API Reference

REST API endpoints and integration

  • POST /api/remote/run
  • GET /api/remote/status
  • GET /api/remote/jobs
  • Webhook callbacks
  • Job tracking

Advanced Pipelines

Creating and customizing workflows

  • Workflow YAML syntax
  • Pipeline dependencies
  • Parallel execution
  • Tool integration
  • Parameter configuration

Example Workflow

name: RNA-seq Pipeline
description: Complete RNA-seq analysis
steps:
  - name: qc
    tool: fastqc
    args:
      input_file: raw_data/sample.fastq
      output_dir: qc/
  
  - name: align
    tool: hisat2
    depends_on: [qc]
    args:
      index: genome_index
      input_fastq1: raw_data/sample.fastq
      output_sam: processed/sample.sam
  
  - name: convert
    tool: samtools
    depends_on: [align]
    args:
      input_sam: processed/sample.sam
      output_bam: processed/sample.bam

Project Structure

Your projects automatically get organized with separate directories for raw data, QC results, processing files, results, reports, logs, and configs.

Parallel Execution

BioBuntu automatically identifies independent pipeline steps and executes them in parallel for faster analysis.

Tool Wrappers

Built-in wrappers for popular bioinformatics tools make integration seamless and configuration simple.