x86 Bioinformatics Setup

This script installs all dependencies necessary to manage different Python versions via Pyenv and Conda, in order to use bioinformatics tools that require x86_64 architecture. Originally designed for ARM64 Macs (Apple Silicon, M1-M3 processors), it now supports multiple platforms and architectures.

Features

• Multi-platform support: Works on macOS (both ARM64 and x86_64) and Linux (Arch-based distributions)
• Automatic detection: Detects OS and architecture automatically
• Force options: Can force specific platform/architecture configurations
• Allows to run packages such as bowtie and macs2 that are not –or not fully– supported in arm64
• Installs R to run scripts locally within hybrid pipelines, but not Rstudio which only recognises the default R version (check the Rig repository to manage different versions of R in Rstudio)
• Automatically installs Bioconductor packages (DESeq2, edgeR, etc.) within the conda environment using BiocManager

Supported Platforms

Platform	Architecture	Status	Notes
macOS	ARM64 (M1-M3)	✅ Supported	Uses Rosetta 2 for x86_64 packages
macOS	x86_64	✅ Supported	Native support
Linux	x86_64	✅ Supported	Arch-based distros only
Linux	ARM64	✅ Supported	Arch-based distros only
Ubuntu/Debian	Any	⚠️ Not yet supported	Would require apt-get integration
RHEL/Fedora	Any	⚠️ Not yet supported	Would require dnf/yum integration

Installation

Basic Installation

Clone this repository, move into it and make the script executable:

git clone <repository-url>
cd x86_bioinformatics_setup
chmod +x ./multiplatform_setup.sh

Then run it with:

./multiplatform_setup.sh

Installation Options

The script supports several command-line options:

# Use fish shell configuration instead of zsh (default)
./multiplatform_setup.sh --fish

# Force specific platform (useful for testing or containers)
./multiplatform_setup.sh --force-platform=linux

# Force specific architecture
./multiplatform_setup.sh --force-arch=x86_64

# Combine multiple options
./multiplatform_setup.sh --fish --force-platform=darwin --force-arch=arm64

# Show help
./multiplatform_setup.sh --help

Platform-Specific Notes

macOS (ARM64/Apple Silicon)

• The script will automatically use Rosetta 2 to run x86_64 bioinformatics packages
• Homebrew will be installed if not present
• Conda environment uses osx-64 subdirectory for compatibility

macOS (x86_64/Intel)

• Native support for all packages
• Homebrew will be installed if not present
• Conda environment uses native osx-64 subdirectory

Linux (Arch-based)

• Supports Arch Linux, Manjaro, EndeavourOS, and other Arch-based distributions
• Uses pacman for system dependencies
• Pyenv is installed via the official installer script
• Miniconda is downloaded and installed to $HOME/miniconda3

Unsupported Linux Distributions

If you're using a non-Arch-based Linux distribution, the script will detect this and provide an informative error message. Support for other distributions can be added by extending the package manager detection logic.

What Gets Installed

Package Managers & Environment Tools

• Homebrew (macOS only)
• Pyenv for Python version management
• Miniconda for conda environment management

Python Versions

• Python 3.12.6 (set as global)
• Python 3.9.7 (for bioinformatics environment)

Bioinformatics Tools

Core tools installed via conda-forge and bioconda:

• bedtools, bowtie, bowtie2, bwa
• hisat2, multiqc, samtools, qualimap
• fastqc, macs2, stringtie, vcftools, kallisto
• snakemake (workflow management system)
• NCBI datasets CLI

Scientific Python Packages

• NumPy, Pandas, SciPy, scikit-learn
• Jupyter, IPython kernel
• Scanpy, HTSeq

R and R Packages

• R base and essentials
• BiocManager for package management
• tidyverse, ggplot2, dplyr
• Seurat
• Bioconductor packages (installed via BiocManager within conda environment):
  • DESeq2, edgeR, limma (RNA-seq differential expression)
  • Rsubread (read alignment and counting)
  • recount3 (access to RNA-seq databases)

Shell Configuration

The script automatically configures your shell. Supported shells:

• Zsh (default on modern macOS)
• Bash (common on Linux)
• Fish (use --fish flag)

After installation, restart your terminal or source your shell configuration:

# For zsh
source ~/.zshrc

# For bash
source ~/.bashrc

# For fish
source ~/.config/fish/config.fish

Usage

After installation, activate the bioinformatics environment:

conda activate bioinformatics

To deactivate:

conda deactivate

Troubleshooting

Platform Detection Issues

If the script incorrectly detects your platform or architecture, use the force options:

./multiplatform_setup.sh --force-platform=linux --force-arch=x86_64

Conda Environment Issues

If packages fail to install due to architecture conflicts, the script will automatically handle the conda subdirectory configuration. For manual fixes:

conda config --env --set subdir osx-64  # For x86_64 on Mac
conda config --env --set subdir linux-64  # For x86_64 on Linux

Bioconductor Package Installation

Some Bioconductor packages (DESeq2, edgeR, limma, etc.) are automatically installed within the conda environment using BiocManager during setup. This approach is used because conda recipes for these packages are outdated and require ancient R versions. If any fail during setup, you can manually install them:

conda activate bioinformatics
Rscript install_r_packages.R
# Or within R:
BiocManager::install(c("DESeq2", "edgeR", "limma"))

Missing Dependencies on Linux

For Arch-based systems, ensure your system is up-to-date:

sudo pacman -Syu

Legacy Script

The original ARM64-only script (arm64_setup.sh) has been deprecated in favor of the new multi-platform multiplatform_setup.sh. While the file is preserved locally for backwards compatibility, it is no longer tracked in version control. Please use multiplatform_setup.sh for all new installations.

License

This project is licensed under the MIT License. Feel free to use and modify the code as per your needs.