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antismash 7.1.0.1 (new formula) #1682

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antismash 7.1.0.1 (new formula) #1682

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antismash 7.1.0.1 (new formula)
YoshitakaMo Apr 30, 2024
c3e8c87
antismash 7.1.0.1 (new formula)
YoshitakaMo Apr 30, 2024
f767b0f
antismash 7.1.0.1 (new formula)
YoshitakaMo Apr 30, 2024
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185 changes: 185 additions & 0 deletions Formula/antismash.rb
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class Antismash < Formula
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"

depends_on "cmake" => :build # scikit-learn
depends_on "pkg-config" => :build
depends_on "rust" => :build # for nrpys
depends_on "blast"
depends_on "brewsci/bio/glimmerhmm"
depends_on "brewsci/bio/hmmer@2"
depends_on "brewsci/bio/[email protected]"
depends_on "brewsci/bio/muscle"
depends_on "diamond"
depends_on "fasttree"
depends_on "hmmer"
depends_on "numpy"
depends_on "prodigal"
depends_on "python-matplotlib"
depends_on "[email protected]"
depends_on "scipy"

on_linux do
depends_on "patchelf" => :build
depends_on "freetype"
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 "helperlibs" do
url "https://files.pythonhosted.org/packages/b6/8a/dd905312ab030099c693966fd47947610251bcd3ac98ef76d16996388a68/helperlibs-0.2.1.tar.gz"
sha256 "4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732"
end

resource "kiwisolver" do
url "https://files.pythonhosted.org/packages/b9/2d/226779e405724344fc678fcc025b812587617ea1a48b9442628b688e85ea/kiwisolver-1.4.5.tar.gz"
sha256 "e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec"
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 "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 "pillow" do
url "https://files.pythonhosted.org/packages/ef/43/c50c17c5f7d438e836c169e343695534c38c77f60e7c90389bd77981bc21/pillow-10.3.0.tar.gz"
sha256 "9d2455fbf44c914840c793e89aa82d0e1763a14253a000743719ae5946814b2d"
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/88/00/835e3d280fdd7784e76bdef91dd9487582d7951a7254f59fc8004fc8b213/scikit-learn-1.3.2.tar.gz"
sha256 "a2f54c76accc15a34bfb9066e6c7a56c1e7235dda5762b990792330b52ccfb05"
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
(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
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