72 lines
2.4 KiB
Ruby
72 lines
2.4 KiB
Ruby
class Sratoolkit < Formula
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desc "Data tools for INSDC Sequence Read Archive"
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homepage "https://github.com/ncbi/sra-tools"
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url "https://github.com/ncbi/sra-tools/archive/2.9.0.tar.gz"
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sha256 "fbdbbf69cf95afca311b9759e14a991dafcb95549ffd5e2e21fb0ecc99fa06aa"
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head "https://github.com/ncbi/sra-tools.git"
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bottle do
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cellar :any
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sha256 "c7f266cafb38da2d4a97f7dd55495bffaee1b4de10dabfff0cd2169feb294c92" => :high_sierra
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sha256 "77c82b91cc83271178381d0787d7f0242cb56c44119c9e07426c25dea7a2e689" => :sierra
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sha256 "3ce0a6f82a5b18b891adac99f1fedf1a941e54356989d8e076bbe7df17b62dc0" => :el_capitan
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end
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depends_on "hdf5"
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depends_on "libmagic"
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resource "ngs-sdk" do
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url "https://github.com/ncbi/ngs/archive/2.9.0.tar.gz"
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sha256 "7e4f9e4490309b6fb33ec9370e5202ad446b10b75c323ba8226c29ca364a0857"
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end
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resource "ncbi-vdb" do
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url "https://github.com/ncbi/ncbi-vdb/archive/2.9.0.tar.gz"
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sha256 "40fdd0a34592f76bdad174d3c2b57b3efcd1e2240512a383bd6e6263b33a6146"
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end
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def install
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ngs_sdk_prefix = buildpath/"ngs-sdk-prefix"
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resource("ngs-sdk").stage do
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cd "ngs-sdk" do
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system "./configure",
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"--prefix=#{ngs_sdk_prefix}",
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"--build=#{buildpath}/ngs-sdk-build"
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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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ncbi_vdb_source = buildpath/"ncbi-vdb-source"
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ncbi_vdb_build = buildpath/"ncbi-vdb-build"
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ncbi_vdb_source.install resource("ncbi-vdb")
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cd ncbi_vdb_source do
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system "./configure",
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"--prefix=#{buildpath/"ncbi-vdb-prefix"}",
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"--with-ngs-sdk-prefix=#{ngs_sdk_prefix}",
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"--build=#{ncbi_vdb_build}"
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ENV.deparallelize { system "make" }
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end
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# Fix the error: ld: library not found for -lmagic-static
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# Upstream PR: https://github.com/ncbi/sra-tools/pull/105
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inreplace "tools/copycat/Makefile", "-smagic-static", "-smagic"
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system "./configure",
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"--prefix=#{prefix}",
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"--with-ngs-sdk-prefix=#{ngs_sdk_prefix}",
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"--with-ncbi-vdb-sources=#{ncbi_vdb_source}",
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"--with-ncbi-vdb-build=#{ncbi_vdb_build}",
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"--build=#{buildpath}/sra-tools-build"
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system "make", "install"
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# Remove non-executable files.
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rm_r [bin/"magic", bin/"ncbi"]
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end
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test do
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assert_match "Read 1 spots for SRR000001", shell_output("#{bin}/fastq-dump -N 1 -X 1 SRR000001")
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assert_match "@SRR000001.1 EM7LVYS02FOYNU length=284", File.read("SRR000001.fastq")
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end
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end
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