82 lines
2.9 KiB
Ruby
82 lines
2.9 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/2.11.0.tar.gz"
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sha256 "10ac0a4d1fafc274bc107de811891d3e803d0713a247581dece4448231883810"
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license all_of: [:public_domain, "GPL-3.0-or-later", "MIT"]
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head "https://github.com/ncbi/sra-tools.git"
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bottle do
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sha256 cellar: :any_skip_relocation, big_sur: "87602a3b77c5d58a037bf2e93423e6cb925bd586fe424680035885894359aeb0"
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sha256 cellar: :any_skip_relocation, catalina: "15a8306c7a3b550ee120a0eb6ab7c87e0e53a3f33549a0a0f3c5a218c6e75d13"
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sha256 cellar: :any_skip_relocation, mojave: "b9b36c564d65e79d3726e4de473e18d892f109221f45dbb91768ecac5758df59"
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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/2.11.0.tar.gz"
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sha256 "5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc"
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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/2.11.0.tar.gz"
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sha256 "9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa"
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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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# For testing purposes, generate a sample config noninteractively in lieu of running vdb-config --interactive
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# See upstream issue: https://github.com/ncbi/sra-tools/issues/291
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require "securerandom"
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mkdir ".ncbi"
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(testpath/".ncbi/user-settings.mkfg").write "/LIBS/GUID = \"#{SecureRandom.uuid}\"\n"
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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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