77 lines
2.3 KiB
Ruby
77 lines
2.3 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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sha256 arm64_big_sur: "e216b2d4b0c1950faedfe6a32dfcedecc524be9f237cdf09450e9fac7414f1e1"
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sha256 big_sur: "4e12ddaa5006c50497f9ad77f18f1b971db88c8b7e2de15f229661611a0a8772"
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sha256 catalina: "81cf9bbb6066d31f5018f3697b9872f051efd99b4de5379924997eee7a2becb2"
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sha256 mojave: "f4f05cdbb102aa7597865c2dd42372181577f00a7aaac7be9f2f315714d5f352"
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sha256 x86_64_linux: "a3284452baea3a3a9d7b078f642e267eb2bd0f1612502313994ac7a8f44aa303"
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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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--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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