55 lines
2 KiB
Ruby
55 lines
2 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+/2.10.0/ncbi-blast-2.10.0+-src.tar.gz"
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version "2.10.0"
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sha256 "3acdd9cec01c4f43e56aeaf89049cb8f8013d60b9c1705eced10166967f1d926"
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bottle do
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rebuild 1
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sha256 "71ebf77b85de24cac6384b796b7b6a70fcaaeded84e1534bbfc4ba86030289d8" => :catalina
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sha256 "4da358f7b8d0fdc4b3d3a47ee16e0f6345c0846d76a692bdfeb7a7e0f84a12dd" => :mojave
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sha256 "0f8ce869239db65218854d9897bc47108d08a33d4f35d7afb56c22f1dc4a24ba" => :high_sierra
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end
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depends_on "lmdb"
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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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