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/2.9.1-1.tar.gz"
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version "2.9.1-1"
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sha256 "561dea9bb00f76a6f9a65cb20d6794379353d02a9e33b0db4f10eb38a42465db"
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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 "341b131b3985cd604bca8fe4cda0f09184b6e6c744be37b7d36a7ef4708d2a70" => :high_sierra
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sha256 "0a06b37706ab390130cba0e529ff9ba666b74bd747068b32771fd9484f4080c7" => :sierra
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sha256 "6e25f614ce455865635ed1a477212a097c7d9d1ccd95aa18a4aa850cdde5c5b8" => :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/2.9.1.tar.gz"
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sha256 "c24c93bd70ed198a44c6b9dba0d6704edc90f228f832f2fef21fa5342303fc50"
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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/2.9.1-1.tar.gz"
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version "2.9.1-1"
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sha256 "c1ee7443599d2cedab13eb44af0a2d29a4c3e8bf0130c2a6b34a9aa7016287e4"
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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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