43 lines
1.5 KiB
Ruby
43 lines
1.5 KiB
Ruby
class Bcftools < Formula
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desc "Tools for BCF/VCF files and variant calling from samtools"
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homepage "http://www.htslib.org/"
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url "https://github.com/samtools/bcftools/releases/download/1.6/bcftools-1.6.tar.bz2"
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sha256 "293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982"
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bottle do
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sha256 "d4371f90c99fec2a9e55a3d8b138a511209105a8e32cac39ffb25bdc0e487b10" => :high_sierra
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sha256 "d451c2fa5530db082ac1a6e015fb9895a51bccf2a89fd381afc781a7d3c2d8a1" => :sierra
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sha256 "fe3bf73cbb6412fef8270a4aae84cf5309d6221909d8f274ffe46a0e1c98d514" => :el_capitan
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end
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depends_on "gsl"
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depends_on "htslib"
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depends_on "xz"
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def install
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# Remove for > 1.6
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# Reported 2 Oct 2017 https://github.com/samtools/bcftools/issues/684
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inreplace "Makefile",
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"PLUGIN_FLAGS = -bundle -bundle_loader bcftools",
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"PLUGIN_FLAGS = -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup"
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system "./configure", "--prefix=#{prefix}",
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"--with-htslib=#{Formula["htslib"].opt_prefix}",
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"--enable-libgsl"
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# Fix install: cannot stat ‘bcftools’: No such file or directory
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# Reported 21 Dec 2017 https://github.com/samtools/bcftools/issues/727
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system "make"
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system "make", "install"
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pkgshare.install "test/query.vcf"
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end
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test do
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output = shell_output("#{bin}/bcftools stats #{pkgshare}/query.vcf")
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assert_match "number of SNPs:\t3", output
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assert_match "fixploidy", shell_output("#{bin}/bcftools plugin -l")
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end
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end
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