📦 Request to Add Formula: Bismark

[BenjaminDEMAILLE]

📦 Request to Add Formula: Bismark

Hi Homebrew Science team,

I’d like to request the addition of a formula for Bismark, a widely used tool for bisulfite-treated sequence alignment and methylation calling.

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🔍 Tool Overview

• Name: bismark
• Version: 0.24.2 (latest as of March 2025)
• Repository: https://github.com/FelixKrueger/Bismark
• License: GNU GPL v3.0
• Language: Perl
• Dependencies: Bowtie2 or HISAT2, Samtools
• Platform: Linux and macOS
• Distribution: Perl scripts + helper utilities

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💡 Why it’s useful

Bismark is the de facto standard for:

• Mapping bisulfite-treated sequencing reads (BS-seq, WGBS)
• Calling methylation levels
• Visualizing CpG/CHH/CHG methylation

It supports both single-end and paired-end reads and can integrate smoothly into methylation analysis pipelines. A Homebrew formula would make it much easier to install and version in reproducible environments and teaching setups.

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⚙️ Dependencies

• bowtie2 or hisat2
• samtools
• perl (system default is usually fine)

All dependencies are already available via Homebrew.

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✅ Proposed Formula

class Bismark < Formula
  desc "Aligner and methylation caller for bisulfite-treated sequencing reads"
  homepage "https://www.bioinformatics.babraham.ac.uk/projects/bismark/"
  url "https://github.com/FelixKrueger/Bismark/archive/refs/tags/v0.24.2.tar.gz"
  sha256 "<insert_sha256_here>"
  license "GPL-3.0-or-later"

  depends_on "bowtie2"
  depends_on "samtools"
  uses_from_macos "perl"

  def install
    bin.install Dir["*.pl"]
    bin.install Dir["*.sh"]
    pkgshare.install "Bisulfite_Genome", "bismark2report", "bismark2summary", "methylation_extractor_examples"
  end

  def caveats
    <<~EOS
      To use Bismark, make sure your reference genome is indexed with:
        bismark_genome_preparation /path/to/genome/

      Then align reads using:
        bismark /path/to/genome -1 sample_R1.fq -2 sample_R2.fq

      For methylation extraction:
        bismark_methylation_extractor aligned_reads.bam

      Full documentation: https://github.com/FelixKrueger/Bismark
    EOS
  end

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

Let me know if you’d prefer that I submit this as a pull request, or if it should go in a separate tap due to its bioinformatics specificity.

Thanks for your great work maintaining Homebrew Science for the research community!

Best regards,