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/2.9.2.tar.gz"
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sha256 "e055091ee1c0b8163c6e470d24e11575884a3c7e829759be38d2239366c3cf3b"
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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 "e373ab7cf39dfa7e16617a2feba8891c989636b1f14198b07f2eb6cf1ba17017" => :high_sierra
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sha256 "27aeefe066364af422c9c9e061d796b76ab477af2690638711d2d0dfe5226327" => :sierra
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sha256 "096a4808717950092b3a64f7d9cc168190b9c4e513243c55b8ba688588a99a45" => :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/2.9.2.tar.gz"
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sha256 "ac559009b2021f56bbfaea680c8207f1608637435136277dad9796516be0385a"
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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/2.9.2.tar.gz"
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sha256 "7db26cc71f7742e693ba8cff8b06fefd2244f42bda4dba4ab315aaea9b9194f0"
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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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