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Installation Guide

This comprehensive guide covers installing Mycelia on various platforms and environments.

Quick Start

For most users, the simplest installation method is:

using Pkg
Pkg.add(url="https://github.com/cjprybol/Mycelia.git")

Table of Contents

  1. System Requirements
  2. Prerequisites
  3. Installation Methods
  4. Platform-Specific Instructions
  5. HPC and Cluster Setup
  6. Docker Installation
  7. Development Installation
  8. Verifying Installation
  9. Common Issues

System Requirements

  • Julia: Latest stable version
  • RAM: 32 GB or more (for genomic datasets)
  • Storage: 50 GB free space
  • CPU: Multi-core processor for parallel operations

For Large-Scale Assembly

  • RAM: 64-256 GB depending on genome size
  • Storage: 500 GB+ free space
  • CPU: 16+ cores recommended

Prerequisites

Julia Installation

  1. Download Julia from julialang.org
  2. Install Julia following platform-specific instructions
  3. Verify installation:
    julia --version

Optional Dependencies

Some features require additional software:

  • Bioconda tools (for external tool integration)
  • Git (for development installation)

Installation Methods

Method 1: Direct Package Installation (Recommended)

using Pkg
Pkg.add(url="https://github.com/cjprybol/Mycelia.git")

Method 2: Development Installation

git clone https://github.com/cjprybol/Mycelia.git
cd Mycelia
julia --project=.

In Julia REPL:

using Pkg
Pkg.instantiate()

Verifying Installation

Run Test Suite

using Pkg
Pkg.test("Mycelia")

Quick Assembly Test

import Mycelia

# Download test data
ref_file = Mycelia.download_genome_by_accession(accession="NC_001422.1")

# Simulate reads
reads_file = Mycelia.simulate_pacbio_reads(
    fasta=ref_file,
    quantity="10x"
)

Next Steps