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

Minimum Requirements

  • Julia: Version 1.10 or higher
  • RAM: 8 GB (for small datasets)
  • Storage: 2 GB free space
  • OS: Linux
  • 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: SSD with 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)
  • C compiler (for some dependencies)

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

using 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"
)

# Run assembly
results = Mycelia.mycelia_assemble(reads_file, max_k=31)

Common Issues

Issue: Package Installation Fails

Symptom: Error during Pkg.add()

Solutions:

  1. Update Julia: juliaup update (if using juliaup)
  2. Clear package cache: rm -rf ~/.julia/compiled
  3. Update registry: Pkg.Registry.update()

Issue: Missing Dependencies

Symptom: Package load errors

Solutions:

using Pkg
Pkg.resolve()
Pkg.instantiate()

Next Steps