60 lines
2.0 KiB
Ruby
60 lines
2.0 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+/2.10.1/ncbi-blast-2.10.1+-src.tar.gz"
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version "2.10.1"
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sha256 "110729decf082f69b90b058c0cabaea38f771983a564308ae19cb30a68ce7b86"
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license "LGPL-2.1"
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bottle do
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sha256 "652c133a61840c1a1f69de4f5827bd358434f3d7caa7886c273b3bab034e0721" => :catalina
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sha256 "b544b1e6e510c0c72b82b581a17eb8704ad53e46e9574d4dfd24bef8f5044148" => :mojave
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sha256 "9dd8d68f78e3825fc33064bc3b79d6474d56593e7260d39ab5f6408ad2e1e939" => :high_sierra
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end
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depends_on "lmdb"
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uses_from_macos "cpio" => :build
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uses_from_macos "bzip2"
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uses_from_macos "zlib"
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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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# Use ./configure --without-boost to fix
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# error: allocating an object of abstract class type 'ncbi::CNcbiBoostLogger'
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# Boost is used only for unit tests.
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# See https://github.com/Homebrew/homebrew-science/pull/3537#issuecomment-220136266
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system "./configure", "--prefix=#{prefix}",
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"--without-debug",
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"--without-boost"
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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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