📦 Request to Add Formula: Cell Ranger

[BenjaminDEMAILLE]

Hi Homebrew Science team,

I’d like to request the addition of a formula (or tap) for Cell Ranger, the official analysis software suite from 10x Genomics for single-cell RNA-seq data processing.

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🔍 Tool Overview

• Name: cellranger
• Version: 9.0.1
• Source: https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
• Vendor: 10x Genomics
• License: Proprietary (free for academic use, but not open-source)
• Platform: Linux only (official), though macOS builds can work via Docker or compatibility layers
• Languages: C++, Python
• Installer: Precompiled binary tarball provided by 10x Genomics

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💡 Why it’s useful

Cell Ranger is the standard toolkit for processing 10x Genomics single-cell RNA-seq data, including:

• Demultiplexing (cellranger mkfastq)
• Alignment and gene counting (cellranger count)
• Aggregation (cellranger aggr)
• Multi-modal analysis (cellranger multi)

It’s widely used in both research and clinical contexts, and having it installable via Homebrew would:

• Simplify installation in reproducible environments (especially CI/CD, Docker, clusters)
• Allow consistent version management alongside other bioinformatics tools
• Improve accessibility for users on Linux (and potentially macOS with workarounds)

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🚫 Licensing Consideration

Because Cell Ranger is not open-source, the formula would likely need to:

• Download the binary from the official 10x Genomics site after user login or EULA acceptance
• Provide a caveats section with installation instructions
• Possibly use a --with-local-tarball option to install from a user-provided .tar.gz

This approach mirrors how other proprietary packages (e.g., CUDA, Intel OneAPI) are handled in Homebrew or custom taps.

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✅ Proposed Formula Structure (if permitted)

class Cellranger < Formula
  desc "10x Genomics single-cell RNA-seq analysis software"
  homepage "https://support.10xgenomics.com/single-cell-gene-expression/software"
  version "9.0.1"
  license :cannot_represent

  # User must manually download and provide the tarball
  url "file://#{HOMEBREW_CACHE}/cellranger-9.0.1.tar.gz"
  sha256 "<computed_sha256_here>"

  def install
    prefix.install Dir["*"]
    bin.install_symlink Dir["#{prefix}/cellranger"]
  end

  def caveats
    <<~EOS
      Due to licensing restrictions, you must manually download the Cell Ranger v9.0.1 tarball from:
        https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest

      After downloading, rename the file to:
        cellranger-9.0.1.tar.gz

      Then place it in:
        #{HOMEBREW_CACHE}/cellranger-9.0.1.tar.gz

      Finally, run:
        brew install --build-from-source cellranger

      This formula installs the precompiled binary and makes it available via the 'cellranger' command.
    EOS
  end

  test do
    system "#{bin}/cellranger", "--help"
  end
end