74 lines
2.5 KiB
Ruby
74 lines
2.5 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/2.10.0.tar.gz"
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sha256 "6d2b02bad674cde6b9677a522f62da092da5471d23738976abce8eae5710fa0c"
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head "https://github.com/ncbi/sra-tools.git"
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bottle do
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cellar :any_skip_relocation
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sha256 "5666b45a693e675a145503ee348aa9be199b6dd53d8e3582e6a2af2f4f647b94" => :catalina
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sha256 "8d9a22d8cc446e66d66b44e8d8e2bbdf60faaa9cc8166e9c7cad1dd5e98abf8b" => :mojave
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sha256 "3dc2db39ac207dc8ba786ba808105cba4128cc9cb5573a02c28e9a71208886c9" => :high_sierra
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end
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depends_on "hdf5"
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depends_on "libmagic"
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uses_from_macos "libxml2"
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uses_from_macos "perl"
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resource "ngs-sdk" do
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url "https://github.com/ncbi/ngs/archive/2.10.0.tar.gz"
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sha256 "4139adff83af213d7880bc80d1c0f5ee9b00c6c4e615d00aa47aaa267e40ed25"
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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/2.10.0.tar.gz"
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sha256 "a6cc88e8d12f536dc96d5f60698d0ef4cf2f63e31d3d12d23da39b1de39563e1"
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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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