Revert removed formulae

Formula/antismash.rb

@@ -0,0 +1,215 @@
+class Antismash < Formula
+  # cite Medema_2011: "https://doi.org/10.1093/nar/gkr466"
+  # cite Blin_2013: "https://doi.org/10.1093/nar/gkt449"
+  # cite Weber_2015: "https://doi.org/10.1093/nar/gkv437"
+  # cite Blin_2017: "https://doi.org/10.1093/nar/gkx319"
+  # cite Blin_2019: "https://doi.org/10.1093/nar/gkz310"
+  # cite Blin_2021: "https://doi.org/10.1093/nar/gkab335"
+  # cite Blin_2023: "https://doi.org/10.1093/nar/gkad344"
+  include Language::Python::Virtualenv
+
+  desc "Antibiotics & Secondary Metabolite Analysis SHell"
+  homepage "https://antismash.secondarymetabolites.org/"
+  url "https://github.com/antismash/antismash/archive/refs/tags/7-1-0-1.tar.gz"
+  version "7.1.0.1"
+  sha256 "1429986c369a81a7c1c60f2cb6efb1a28eacdb0290ec9c933477bad88d2b839d"
+  license "AGPL-3.0-or-later"
+  head "https://github.com/antismash/antismash.git", branch: "master"
+
+  bottle do
+    root_url "https://ghcr.io/v2/brewsci/bio"
+    sha256 cellar: :any,                 arm64_sonoma: "2ff34ee73fed805df8886ccd8df52f44954f6571f5784a08f9445c62f2af8080"
+    sha256 cellar: :any,                 ventura:      "afaa9fe5de6ba026dc2b24ef5846cdb19c00b3628c395576388e42c626426b7b"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "e55dbefa5f83597be56a296f7e34c4de395e949d57f9428de5d725824224511e"
+  end
+
+  depends_on "cmake" => :build # scikit-learn
+  depends_on "meson" => :build
+  depends_on "ninja" => :build
+  depends_on "pkg-config" => :build
+  depends_on "rust" => :build # for nrpys
+  depends_on "blast"
+  depends_on "brewsci/bio/fasttree"
+  depends_on "brewsci/bio/glimmerhmm"
+  depends_on "brewsci/bio/hmmer@2"
+  depends_on "brewsci/bio/meme@4.11.2"
+  depends_on "brewsci/bio/muscle"
+  depends_on "ca-certificates"
+  depends_on "cython"
+  depends_on "diamond"
+  depends_on "freetype"
+  depends_on "hmmer"
+  depends_on "jpeg-turbo"
+  depends_on "libtiff"
+  depends_on "little-cms2"
+  depends_on "numpy"
+  depends_on "pillow"
+  depends_on "prodigal"
+  depends_on "python-matplotlib"
+  depends_on "python@3.12"
+  depends_on "scipy"
+
+  on_macos do
+    depends_on "libomp"
+  end
+
+  on_linux do
+    depends_on "patchelf" => :build
+    depends_on "ca-certificates"
+  end
+
+  resource "attrs" do
+    url "https://files.pythonhosted.org/packages/e3/fc/f800d51204003fa8ae392c4e8278f256206e7a919b708eef054f5f4b650d/attrs-23.2.0.tar.gz"
+    sha256 "935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"
+  end
+
+  resource "bcbio-gff" do
+    url "https://files.pythonhosted.org/packages/20/03/769e86d61923c2febd229a9946bbfd0f5bc5ab09237481fb4c71e39d6966/bcbio-gff-0.7.1.tar.gz"
+    sha256 "d1dc3294147b95baced6033f6386a0fed45c43767ef02d1223df5ef497e9cca6"
+  end
+
+  resource "biopython" do
+    url "https://files.pythonhosted.org/packages/89/c5/7fe326081276f74a4073f6d6b13cfa7a04ba322a3ff1d84027f4773980b8/biopython-1.78.tar.gz"
+    sha256 "1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564"
+  end
+
+  resource "brawn" do
+    url "https://files.pythonhosted.org/packages/1a/7d/abd734ec8b452d87f501cb57da1cb55f4ab999e5fe2d570c1f51374c70b5/brawn-1.0.1.tar.gz"
+    sha256 "dd76831a9dee955692082f46209db645bceb2e48509cbe0eeb9d9e20f53cbb6c"
+  end
+
+  resource "contourpy" do
+    url "https://files.pythonhosted.org/packages/8d/9e/e4786569b319847ffd98a8326802d5cf8a5500860dbfc2df1f0f4883ed99/contourpy-1.2.1.tar.gz"
+    sha256 "4d8908b3bee1c889e547867ca4cdc54e5ab6be6d3e078556814a22457f49423c"
+  end
+
+  resource "cycler" do
+    url "https://files.pythonhosted.org/packages/a9/95/a3dbbb5028f35eafb79008e7522a75244477d2838f38cbb722248dabc2a8/cycler-0.12.1.tar.gz"
+    sha256 "88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"
+  end
+
+  resource "fonttools" do
+    url "https://files.pythonhosted.org/packages/67/ac/d7bf44ce57ff5770c267e63cff003cfd5ee43dc49abf677f8b7067fbd3fb/fonttools-4.50.0.tar.gz"
+    sha256 "fa5cf61058c7dbb104c2ac4e782bf1b2016a8cf2f69de6e4dd6a865d2c969bb5"
+  end
+
+  resource "hatchling" do
+    url "https://files.pythonhosted.org/packages/a3/51/8a4a67a8174ce59cf49e816e38e9502900aea9b4af672d0127df8e10d3b0/hatchling-1.25.0.tar.gz"
+    sha256 "7064631a512610b52250a4d3ff1bd81551d6d1431c4eb7b72e734df6c74f4262"
+  end
+
+  resource "helperlibs" do
+    url "https://files.pythonhosted.org/packages/b6/8a/dd905312ab030099c693966fd47947610251bcd3ac98ef76d16996388a68/helperlibs-0.2.1.tar.gz"
+    sha256 "4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732"
+  end
+
+  resource "jinja2" do
+    url "https://files.pythonhosted.org/packages/b2/5e/3a21abf3cd467d7876045335e681d276ac32492febe6d98ad89562d1a7e1/Jinja2-3.1.3.tar.gz"
+    sha256 "ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"
+  end
+
+  resource "joblib" do
+    url "https://files.pythonhosted.org/packages/7c/c3/94c9e4886e8f33832690ab48fdac4a121a7bfec3e2c044c9f2762aa9068e/joblib-1.4.0.tar.gz"
+    sha256 "1eb0dc091919cd384490de890cb5dfd538410a6d4b3b54eef09fb8c50b409b1c"
+  end
+
+  resource "jsonschema" do
+    url "https://files.pythonhosted.org/packages/03/8a/8975198ffd870ab2c04be32d200943a299fdf8a9b8e42b5e027a7a89fe4a/jsonschema-4.11.0.tar.gz"
+    sha256 "706bbcafb49b1350fbcea40b209bdce8aed07c3288f7a77e9539bd5b3ddead3d"
+  end
+
+  resource "kiwisolver" do
+    url "https://files.pythonhosted.org/packages/b9/2d/226779e405724344fc678fcc025b812587617ea1a48b9442628b688e85ea/kiwisolver-1.4.5.tar.gz"
+    sha256 "e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec"
+  end
+
+  resource "libsass" do
+    url "https://files.pythonhosted.org/packages/79/b4/ab091585eaa77299558e3289ca206846aefc123fb320b5656ab2542c20ad/libsass-0.23.0.tar.gz"
+    sha256 "6f209955ede26684e76912caf329f4ccb57e4a043fd77fe0e7348dd9574f1880"
+  end
+
+  resource "markupsafe" do
+    url "https://files.pythonhosted.org/packages/87/5b/aae44c6655f3801e81aa3eef09dbbf012431987ba564d7231722f68df02d/MarkupSafe-2.1.5.tar.gz"
+    sha256 "d283d37a890ba4c1ae73ffadf8046435c76e7bc2247bbb63c00bd1a709c6544b"
+  end
+
+  resource "MOODS-python" do
+    url "https://files.pythonhosted.org/packages/f7/34/c623e9b57e3e3f1edf030201603d8110bf9969921790d950836176be4749/MOODS-python-1.9.4.1.tar.gz"
+    sha256 "b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc"
+  end
+
+  resource "nrpys" do
+    url "https://files.pythonhosted.org/packages/07/4e/fa89f65eb34d685b6d24da6e49c057e8d2f68c7fd2e66e8431ddd3664af2/nrpys-0.1.1.tar.gz"
+    sha256 "eab0e7762ca97109ec701da51b161cc431680fbaeeba5fc6d4cf2c190f69bb7f"
+  end
+
+  resource "packaging" do
+    url "https://files.pythonhosted.org/packages/ee/b5/b43a27ac7472e1818c4bafd44430e69605baefe1f34440593e0332ec8b4d/packaging-24.0.tar.gz"
+    sha256 "eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9"
+  end
+
+  resource "pyparsing" do
+    url "https://files.pythonhosted.org/packages/46/3a/31fd28064d016a2182584d579e033ec95b809d8e220e74c4af6f0f2e8842/pyparsing-3.1.2.tar.gz"
+    sha256 "a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad"
+  end
+
+  resource "pyrsistent" do
+    url "https://files.pythonhosted.org/packages/ce/3a/5031723c09068e9c8c2f0bc25c3a9245f2b1d1aea8396c787a408f2b95ca/pyrsistent-0.20.0.tar.gz"
+    sha256 "4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4"
+  end
+
+  resource "pysvg-py3" do
+    url "https://files.pythonhosted.org/packages/63/92/a0d9d3c3f339bdd7f364e3e85033fc7649bb59d651dbab88ef9774e4cdaf/pysvg-py3-0.2.2.post3.tar.gz"
+    sha256 "a1183aa5d89871298c11f25d28640edc3798b6ed1e2b2a95c30d35985d6431d0"
+  end
+
+  resource "python-dateutil" do
+    url "https://files.pythonhosted.org/packages/66/c0/0c8b6ad9f17a802ee498c46e004a0eb49bc148f2fd230864601a86dcf6db/python-dateutil-2.9.0.post0.tar.gz"
+    sha256 "37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"
+  end
+
+  resource "scikit-learn" do
+    url "https://files.pythonhosted.org/packages/92/72/2961b9874a9ddf2b0f95f329d4e67f67c3301c1d88ba5e239ff25661bb85/scikit_learn-1.5.1.tar.gz"
+    sha256 "0ea5d40c0e3951df445721927448755d3fe1d80833b0b7308ebff5d2a45e6414"
+  end
+
+  resource "six" do
+    url "https://files.pythonhosted.org/packages/71/39/171f1c67cd00715f190ba0b100d606d440a28c93c7714febeca8b79af85e/six-1.16.0.tar.gz"
+    sha256 "1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"
+  end
+
+  resource "threadpoolctl" do
+    url "https://files.pythonhosted.org/packages/bd/55/b5148dcbf72f5cde221f8bfe3b6a540da7aa1842f6b491ad979a6c8b84af/threadpoolctl-3.5.0.tar.gz"
+    sha256 "082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"
+  end
+
+  def python3
+    which("python3.12")
+  end
+
+  def install
+    ENV.append "CPPFLAGS", "-I#{Formula["freetype"].opt_include}/freetype2" if OS.linux?
+    venv = virtualenv_create(libexec, python3)
+    venv.pip_install(resources)
+    site_packages = Language::Python.site_packages(python3)
+
+    venv.pip_install_and_link buildpath
+    # Fix minor warning in BCBio
+    inreplace "#{libexec}/lib/python3.12/site-packages/BCBio/GFF/GFFParser.py",
+              "compile(\"\\w+=\")", "compile(r\"\\w+=\")"
+    (prefix/site_packages/"homebrew-antismash.pth").write venv.site_packages
+  end
+
+  def caveats
+    <<~EOS
+      Run `download-antismash-databases` to download the databases into
+      #{opt_libexec}/lib/python3.12/site-packages/antismash/databases
+      and `antismash --check-prereqs` to check the prerequisites.
+    EOS
+  end
+
+  test do
+    assert_match "antiSMASH", shell_output("#{bin}/antismash -h 2>&1")
+    system python3, "-c", "import antismash"
+  end
+end

Formula/parsnp.rb

@@ -0,0 +1,65 @@
+class Parsnp < Formula
+  # cite Treangen_2014: "https://doi.org/10.1186/s13059-014-0524-x"
+  desc "Microbial core genome alignment and SNP detection"
+  homepage "https://github.com/marbl/parsnp"
+  url "https://github.com/marbl/parsnp/archive/refs/tags/v2.0.5.tar.gz"
+  sha256 "1d23695d0d624fa17e02c43b1d730200e526c17a48615593f75ee8fc35402489"
+  head "https://github.com/marbl/parsnp.git", branch: "master"
+
+  bottle do
+    root_url "https://ghcr.io/v2/brewsci/bio"
+    sha256 cellar: :any,                 arm64_sonoma: "d00efe0566c3c017d36630032599b252e5a19a78c01279fd8bbfba7abdf2045f"
+    sha256 cellar: :any,                 ventura:      "6357c9eac4ac96eebaf8825cbb06eafcd26a30c0a0838b4e673889544683b9dc"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "36a5646f5c4c611c5e1b384541b06f490bb424f34a8e98439ab1e294a708b922"
+  end
+
+  depends_on "autoconf" => :build
+  depends_on "automake" => :build
+  depends_on "libtool" => :build
+  depends_on "pkg-config" => :build
+
+  depends_on "brewsci/bio/fasttree"
+  depends_on "brewsci/bio/harvest-tools"
+
+  uses_from_macos "zlib"
+
+  on_macos do
+    depends_on "libomp"
+  end
+
+  def install
+    # remove binaries
+    rm Dir["bin/*"]
+
+    # https://github.com/marbl/parsnp/issues/52
+    inreplace "src/parsnp.cpp", "1.0.1", version.to_s
+
+    cd "muscle" do
+      ENV.deparallelize
+      system "./autogen.sh"
+      system "./configure", "--prefix=#{prefix}"
+      system "make", "install"
+      (doc/"muscle").install "AUTHORS", "ChangeLog"
+    end
+
+    system "./autogen.sh"
+    system "./configure", "--prefix=#{prefix}", "--with-libmuscle=#{include}"
+
+    # https://github.com/marbl/parsnp/issues/57
+    libr = " -lMUSCLE-3.7"
+    inreplace "src/Makefile", libr, ""
+    inreplace "src/Makefile", "LIBS =", "LIBS =#{libr}"
+    inreplace "src/Makefile", "LDFLAGS = ", "LDFLAGS = -L#{lib}"
+
+    system "make"
+
+    bin.install "src/parsnp_core"
+    bin.install_symlink "parsnp_core" => "parsnp"
+    pkgshare.install "examples"
+    doc.install "CITATION", "LICENSE", "README.md"
+  end
+
+  test do
+    assert_match version.to_s, shell_output("#{bin}/parsnp -v 2>&1")
+  end
+end

Formula/phlawd.rb

@@ -0,0 +1,54 @@
+class Phlawd < Formula
+  # cite Smith_2009: "https://doi.org/10.1186/1471-2148-9-37"
+  desc "Phylogenetic dataset construction"
+  homepage "https://github.com/jonchang/phlawd"
+  url "https://github.com/jonchang/phlawd/archive/refs/tags/3.4b.tar.gz"
+  version "3.4b"
+  sha256 "a0fea43866e425f7fed5f74bcb8c391484a10b486f3f03d5b7bbc4df84dd84b8"
+  license "GPL-2.0"
+  revision 2
+
+  bottle do
+    root_url "https://ghcr.io/v2/brewsci/bio"
+    sha256 cellar: :any_skip_relocation, catalina:     "ece6f29b1e9ae8f93d7e0cbf041f1bad949c68955f02ca9f0dbb0279d4b3d7b8"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "d93ccf2fdc9de7917a96a99c153983c8d8c5798b35a4e63ff247ab54fcdbb061"
+  end
+
+  depends_on "brewsci/bio/muscle"
+  depends_on "brewsci/bio/quicktree"
+  depends_on "libomp" if OS.mac?
+  depends_on "mafft"
+  depends_on "wget"
+
+  uses_from_macos "sqlite"
+
+  def install
+    ENV.append_to_cflags "-mmacosx-version-min=10.12 -lomp" if OS.mac?
+    sql = OS.mac? ? "sqlitewrapped-1.3.1.MAC.tgz" : "sqlitewrapped-1.3.1.tar.gz"
+
+    cd "deps" do
+      system "tar", "xf", sql, "--strip-components=1"
+      system "make"
+    end
+
+    cd "src" do
+      inreplace "Makefile.in" do |s|
+        s.gsub! "fopenmp", "fopenmp @CFLAGS@"
+        s.gsub! "deps/$(HOST)", "deps"
+      end
+
+      if OS.mac?
+        system "./configure", "ac_cv_prog_cxx_openmp=-Xpreprocessor -fopenmp"
+      else
+        system "./configure"
+      end
+
+      system "make"
+      bin.install "PHLAWD"
+    end
+  end
+
+  test do
+    assert_match version.to_s, shell_output("#{bin}/PHLAWD")
+  end
+end

Formula/pirate.rb

@@ -0,0 +1,41 @@
+class Pirate < Formula
+  # cite Bayliss_2019: "https://doi.org/10.1101/598391"
+  desc "Pangenome analysis and threshold evaluation toolbox"
+  homepage "https://github.com/SionBayliss/PIRATE"
+  url "https://github.com/SionBayliss/PIRATE/archive/refs/tags/v1.0.5.tar.gz"
+  sha256 "d5d7e657558eadae301a3198bccfd5ee04daddab1a872049d8a74cb71c35f20b"
+  license "GPL-3.0-or-later"
+
+  bottle do
+    root_url "https://ghcr.io/v2/brewsci/bio"
+    sha256 cellar: :any_skip_relocation, arm64_sonoma: "f9c3d3f37065a05791b6c561888fbe9e3f532320a45c312018ae4130cd3fb853"
+    sha256 cellar: :any_skip_relocation, ventura:      "f9c3d3f37065a05791b6c561888fbe9e3f532320a45c312018ae4130cd3fb853"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "2a810a4b27460809759ab9c9f2a62a4d58660b6281c9fd87a92b0cbc981c9883"
+  end
+
+  depends_on "bioperl"
+  depends_on "blast"
+  depends_on "brewsci/bio/cd-hit"
+  depends_on "brewsci/bio/fasttree"
+  depends_on "brewsci/bio/mcl"
+  depends_on "diamond"
+  depends_on "mafft"
+  depends_on "parallel"
+
+  uses_from_macos "perl"
+  uses_from_macos "unzip"
+
+  def install
+    ENV.prepend "PERL5LIB", Formula["bioperl"].libexec/"lib/perl5"
+    libexec.install Dir["*"]
+    %w[PIRATE].each do |name|
+      (bin/name).write_env_script("#{libexec}/bin/#{name}", PERL5LIB: ENV["PERL5LIB"])
+    end
+  end
+
+  test do
+    assert_match version.to_s, shell_output("#{bin}/PIRATE --version 2>&1")
+    assert_match "pangenome", shell_output("#{bin}/PIRATE --help 2>&1")
+    system "#{bin}/PIRATE", "--check"
+  end
+end