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tigmint 1.2.10 #2284

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156b998
tigmint 1.2.10
BenjaminDEMAILLE Jul 7, 2026
b998d5d
tigmint: specify head branch (audit)
BenjaminDEMAILLE Jul 7, 2026
bfa4367
tigmint: use Homebrew btllib instead of unsatisfiable pip pin
BenjaminDEMAILLE Jul 10, 2026
1d2d866
tigmint: fix linkage audit and unreachable homepage
BenjaminDEMAILLE Jul 11, 2026
859f97d
tigmint: declare xz linkage dependency on Linux
BenjaminDEMAILLE Jul 11, 2026
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40 changes: 29 additions & 11 deletions Formula/tigmint.rb
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Original file line number Diff line number Diff line change
@@ -1,11 +1,13 @@
class Tigmint < Formula
include Language::Python::Shebang

# cite Jackman_2018: "https://doi.org/10.1186/s12859-018-2425-6"
desc "Correct misassemblies using linked or long reads"
homepage "https://bcgsc.github.io/tigmint/"
url "https://github.com/bcgsc/tigmint/releases/download/v1.2.5/tigmint-1.2.5.tar.gz"
sha256 "15a56748f19732462c0445fe9df2f737a4bf8caa97dbc0fe6e943e3fd1c6b5f0"
homepage "https://github.com/bcgsc/tigmint"
url "https://github.com/bcgsc/tigmint/releases/download/v1.2.10/tigmint-1.2.10.tar.gz"
sha256 "8e7b5d424ff69d5da7b117bef9996463b02205078ce0fb6e3074ca6c9933efa9"
license "GPL-3.0-only"
head "https://github.com/bcgsc/tigmint.git"
head "https://github.com/bcgsc/tigmint.git", branch: "master"

bottle do
root_url "https://ghcr.io/v2/brewsci/bio"
Expand All @@ -14,24 +16,40 @@
end

depends_on "bedtools"
depends_on "btllib"

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tigmint: new dependency impact 

Adding `btllib` adds 1 new recursive dependency on arm64_sequoia (6.9MB).

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tigmint: new dependency impact 

Adding `btllib` adds 1 new recursive dependency on arm64_tahoe (6.9MB).

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tigmint: new dependency impact 

Adding `btllib` adds 1 new recursive dependency on arm64_sonoma (6.9MB).

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tigmint: new dependency impact 

Adding `btllib` adds 1 new recursive dependency on x86_64_linux (8.7MB).
depends_on "libdeflate"
depends_on "minimap2"
depends_on "numpy"
depends_on "python@3.9"
depends_on "python@3.14"

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tigmint: new dependency impact 

Adding `python@3.14` adds 6 new recursive dependencies on arm64_sequoia (122.4MB).

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tigmint: new dependency impact 

Adding `python@3.14` adds 6 new recursive dependencies on arm64_tahoe (122.2MB).

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tigmint: new dependency impact 

Adding `python@3.14` adds 7 new recursive dependencies on arm64_sonoma (123MB).

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tigmint: new dependency impact 

Adding `python@3.14` adds 5 new recursive dependencies on x86_64_linux (86MB).
depends_on "samtools"

on_linux do
depends_on "xz"
depends_on "zlib-ng-compat"
end

def install
ENV.prepend_path "PATH", libexec/"bin"
xy = Language::Python.major_minor_version "python3"
python = formula_opt_bin("python@3.14")/"python3.14"
xy = Language::Python.major_minor_version python
ENV.prepend_path "PYTHONPATH", libexec/"lib/python#{xy}/site-packages"
inreplace "bin/tigmint-cut", "/usr/bin/env python3", Formula["python@3.9"].bin/"python3.9"
inreplace "bin/tigmint_molecule.py", "/usr/bin/env python3", Formula["python@3.9"].bin/"python3.9"
inreplace "bin/tigmint_molecule_paf.py", "/usr/bin/env python3", Formula["python@3.9"].bin/"python3.9"
system "pip3", "install", "--prefix=#{libexec}", "-r", "requirements.txt", "--no-binary=pysam"
# btllib is provided by Homebrew (its PyPI pin is unsatisfiable on modern
# Python) and numpy comes from the numpy formula; drop both from the pip list.
inreplace "requirements.txt" do |s|
s.gsub!(/^btllib\b.*\n/, "")
s.gsub!(/^numpy\b.*\n/, "")
end
system python, "-m", "pip", "install", "--prefix=#{libexec}",
"-r", "requirements.txt", "--no-binary=pysam"
bin.install Dir["bin/*"]
rewrite_shebang python_shebang_rewrite_info(python), *bin.children
system "make", "-C", "src"
libexec_src = Pathname.new("#{libexec}/src")
libexec_src.install "src/long-to-linked-pe"
bin.env_script_all_files libexec/"bin", PYTHONPATH: Dir[libexec/"lib/python*/site-packages"].first
btllib_python = formula_opt_lib("btllib")/"btllib/python"
site_packages = Dir[libexec/"lib/python*/site-packages"].first
bin.env_script_all_files libexec/"bin",
PYTHONPATH: "#{site_packages}#{File::PATH_SEPARATOR}#{btllib_python}"
end

test do
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