snippy 4.6.0 (#1817)

Formula/snippy.rb

@@ -0,0 +1,84 @@
+class Snippy < Formula
+  desc "Rapid bacterial SNP calling and core genome alignments"
+  homepage "https://github.com/tseemann/snippy"
+  url "https://github.com/tseemann/snippy/archive/refs/tags/v4.6.0.tar.gz"
+  sha256 "7264e3819e249387effd3eba170ff49404b1cf7347dfa25944866f5aeb6b11c3"
+  license "GPL-2.0-or-later"
+
+  bottle do
+    root_url "https://ghcr.io/v2/brewsci/bio"
+    sha256 cellar: :any_skip_relocation, catalina:     "8c0d0939812e84c244a2f87a92d42ae79fa9c001ee3a4ea8f00fefa4dd2fd15b"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "c7a253e55f63fa2969d95ff81908f7fc61a6b1b09cc46b9d796511071396251b"
+  end
+
+  depends_on "bcftools"
+  depends_on "bedtools"
+  depends_on "bioperl"
+  depends_on "brewsci/bio/freebayes"
+  depends_on "brewsci/bio/samclip"
+  depends_on "brewsci/bio/snp-sites"
+  depends_on "brewsci/bio/snpeff"
+  depends_on "brewsci/bio/vcflib"
+  depends_on "brewsci/bio/vt"
+  depends_on "bwa"
+  depends_on "minimap2"
+  depends_on "openjdk@11"
+  depends_on "perl"
+  depends_on "samtools"
+  depends_on "seqtk"
+
+  uses_from_macos "bzip2"
+  uses_from_macos "gzip"
+
+  resource "any2fasta" do
+    url "https://raw.githubusercontent.com/tseemann/any2fasta/v0.4.2/any2fasta"
+    sha256 "ed20e895c7a94d246163267d56fce99ab0de48784ddda2b3bf1246aa296bf249"
+  end
+
+  resource "fasta_generate_regions.py" do
+    url "https://raw.githubusercontent.com/tseemann/snippy/master/binaries/noarch/fasta_generate_regions.py"
+    sha256 "6c688cc748cc48fae99a5274dfb7053f446287af36728f5473c8a54721d221e3"
+  end
+
+  def install
+    rm_r "binaries"
+
+    ENV.prepend_path "PERL5LIB", Formula["bioperl"].opt_libexec/"lib/perl5"
+    ENV.prepend_create_path "PERL5LIB", libexec
+    ENV["PERL_MM_USE_DEFAULT"] = "1"
+
+    libexec.install Dir["*"]
+    binaries = %w[
+      snippy
+      snippy-core
+      snippy-vcf_to_tab
+      snippy-clean_full_aln
+      snippy-multi
+      snippy-vcf_extract_subs
+      snippy-vcf_report
+      snippy-vcf_to_tab
+    ]
+    binaries.each do |name|
+      (bin/name).write_env_script("#{libexec}/bin/#{name}",
+                                   JAVA_HOME: Formula["openjdk@11"].opt_prefix,
+                                   PERL5LIB:  ENV["PERL5LIB"])
+    end
+
+    mkdir_p libexec/"binaries/noarch"
+    resources.each do |r|
+      (libexec/"binaries/noarch").install r
+      chmod 0755, libexec/"binaries/noarch/#{r.name}"
+    end
+    inreplace "#{libexec}/binaries/noarch/fasta_generate_regions.py", "/usr/bin/env python", "/usr/bin/env python3"
+  end
+
+  test do
+    assert_match version.to_s, shell_output("#{bin}/snippy --version 2>&1")
+    assert_match version.to_s, shell_output("#{bin}/snippy-core --version 2>&1")
+    assert_match version.to_s, shell_output("#{bin}/snippy-vcf_to_tab --version 2>&1")
+    assert_match version.to_s, shell_output("#{bin}/snippy-clean_full_aln --version 2>&1")
+    system "#{bin}/snippy-multi", "--help"
+    system "#{bin}/snippy", "--check"
+    system "#{bin}/snippy-core", "--check"
+  end
+end