82 lines
2.5 KiB
Ruby
82 lines
2.5 KiB
Ruby
class Blast < Formula
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desc "Basic Local Alignment Search Tool"
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homepage "https://blast.ncbi.nlm.nih.gov/"
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url "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-src.tar.gz"
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version "2.12.0"
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sha256 "fda3c9c9d488cad6c1880a98a236d842bcf3610e3e702af61f7a48cf0a714b88"
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license :public_domain
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livecheck do
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url "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/VERSION"
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regex(/v?(\d+(?:\.\d+)+)/i)
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end
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bottle do
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rebuild 1
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sha256 arm64_big_sur: "2976fc131888183295514f2e2d2ff32c91cc2f15b76361c37d2a9414283c16ff"
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sha256 big_sur: "2fd23535ef7180812f7d16abf25590cc99a1689fc3edcfe1fbb84cd79c65e1a3"
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sha256 catalina: "a044ffeb208ed5b4de37cba25e584b74b571368ad4ed5260155f671981ccd4ae"
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sha256 mojave: "3ccce772ca8ef7f25343f13bd43cc8f12e0d4288306bf6bcde5d2303e112e378"
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sha256 x86_64_linux: "bbc0b4c269fd0899d3506763f48264248af36a367c7fae3a032199be666ed65e"
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end
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depends_on "lmdb"
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uses_from_macos "bzip2"
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uses_from_macos "zlib"
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on_macos do
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depends_on "libomp"
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end
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on_linux do
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depends_on "libarchive" => :build
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end
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conflicts_with "proj", because: "both install a `libproj.a` library"
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def install
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cd "c++" do
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# Boost is only used for unit tests.
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args = %W[--prefix=#{prefix}
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--with-bin-release
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--with-mt
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--with-strip
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--with-experimental=Int8GI
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--without-debug
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--without-boost]
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if OS.mac?
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args += ["OPENMP_FLAGS=-Xpreprocessor -fopenmp",
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"LDFLAGS=-lomp"]
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end
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system "./configure", *args
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# Fix the error: install: ReleaseMT/lib/*.*: No such file or directory
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system "make"
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system "make", "install"
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end
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end
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test do
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output = shell_output("#{bin}/update_blastdb.pl --showall")
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assert_match "nt", output
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(testpath/"test.fasta").write <<~EOS
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>U00096.2:1-70
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AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
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EOS
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output = shell_output("#{bin}/blastn -query test.fasta -subject test.fasta")
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assert_match "Identities = 70/70", output
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# Create BLAST database
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output = shell_output("#{bin}/makeblastdb -in test.fasta -out testdb -dbtype nucl")
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assert_match "Adding sequences from FASTA", output
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# Check newly created BLAST database
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output = shell_output("#{bin}/blastdbcmd -info -db testdb")
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assert_match "Database: test", output
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end
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end
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