61 lines
2.1 KiB
Ruby
61 lines
2.1 KiB
Ruby
class Mmseqs2 < Formula
|
|
desc "Software suite for very fast protein sequence search and clustering"
|
|
homepage "https://mmseqs.org/"
|
|
url "https://github.com/soedinglab/MMseqs2/archive/8-fac81.tar.gz"
|
|
version "8-fac81"
|
|
sha256 "035d1c9a5fcfae50bc2d201f177722bd79d95d3ba32342972baa7b142b52aa82"
|
|
revision 1
|
|
|
|
bottle do
|
|
cellar :any
|
|
sha256 "1453917340436e36566e7404ec973475740d79f06e71cc2b97830cf017b2aaa8" => :mojave
|
|
sha256 "b2a997519dedb4538e31b3ef91efd946a2c0414d71ebef18f529d0f918b7546a" => :high_sierra
|
|
sha256 "578ea72406c8522e5acd29c3d3e596ed653b4a1c26f2accfd78444a0e2848c4f" => :sierra
|
|
end
|
|
|
|
depends_on "cmake" => :build
|
|
depends_on "gcc"
|
|
|
|
cxxstdlib_check :skip
|
|
|
|
fails_with :clang # needs OpenMP support
|
|
|
|
resource "documentation" do
|
|
url "https://github.com/soedinglab/MMseqs2.wiki.git",
|
|
:revision => "a4f660d1bbf5e71438d03e09fa4ca036ceb18128"
|
|
end
|
|
|
|
def install
|
|
args = *std_cmake_args << "-DHAVE_TESTS=0" << "-DHAVE_MPI=0"
|
|
args << "-DVERSION_OVERRIDE=#{version}"
|
|
args << "-DHAVE_SSE4_1=1"
|
|
|
|
# Workaround for issue introduced in macOS 10.14 SDK
|
|
# SDK uses _Atomic in ucred.h which current g++ does not support
|
|
# __APPLE_API_STRICT_CONFORMANCE makes sysctl.h not include apis like ucred.h
|
|
# and thus we dont fail compilation anymore
|
|
# See: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=89864
|
|
args << "-DCMAKE_CXX_FLAGS=-D__APPLE_API_STRICT_CONFORMANCE"
|
|
|
|
system "cmake", ".", *args
|
|
system "make", "install"
|
|
|
|
resource("documentation").stage { doc.install Dir["*"] }
|
|
pkgshare.install "examples"
|
|
bash_completion.install "util/bash-completion.sh" => "mmseqs.sh"
|
|
end
|
|
|
|
def caveats
|
|
unless Hardware::CPU.sse4?
|
|
"MMseqs2 requires at least SSE4.1 CPU instruction support."
|
|
end
|
|
end
|
|
|
|
test do
|
|
system "#{bin}/mmseqs", "createdb", "#{pkgshare}/examples/QUERY.fasta", "q"
|
|
system "#{bin}/mmseqs", "cluster", "q", "res", "tmp", "-s", "1"
|
|
system "#{bin}/mmseqs", "createtsv", "q", "q", "res", "res.tsv"
|
|
assert_predicate testpath/"res.tsv", :exist?
|
|
assert_predicate (testpath/"res.tsv").size, :positive?
|
|
end
|
|
end
|