homebrew-core/Formula/bcftools.rb

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