82 lines
3.4 KiB
Ruby
82 lines
3.4 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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license all_of: [:public_domain, "GPL-3.0-or-later", "MIT"]
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stable do
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url "https://github.com/ncbi/sra-tools/archive/refs/tags/3.0.3.tar.gz"
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sha256 "ea4b9a4b2e6e40e6b2bf36b01eb8df2b50280ef9dcdc66b504c1d1296600afbd"
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resource "ncbi-vdb" do
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url "https://github.com/ncbi/ncbi-vdb/archive/refs/tags/3.0.2.tar.gz"
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sha256 "275ccb225ddb156688c8c71f772f73276cb18ebff773a51150f86f8002ed2d59"
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end
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end
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livecheck do
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url :stable
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regex(/^v?(\d+(?:\.\d+)+)$/i)
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end
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bottle do
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sha256 cellar: :any, arm64_ventura: "9fac24d57962e0b711e915e3603f1fe9e74035ee24ce8fb66a6019ba0cfc39d7"
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sha256 cellar: :any, arm64_monterey: "f3b3de271cc0f04ff40c25d405ede0cafa9b045bcbb5cbf09f9a923b6bb0db95"
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sha256 cellar: :any, arm64_big_sur: "b10a2b505112c1770814aba5a346019cdef789ee4c17ba13e45de006f61c54da"
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sha256 cellar: :any, ventura: "5d643b579db1c5487c23f4091e6603f5d6b3b41b6f082dca9083215d69adc6f3"
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sha256 cellar: :any, monterey: "5ffe635f09dd6398aebfc5a5a1af23f3022b70892bd809ba4b94fc7f738a3de5"
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sha256 cellar: :any, big_sur: "431ccf7fabaeddaffb398447b7d54bf79300d879a6b6cd8e415b35f90f0af501"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "f469089c23a834c41f7bd865a76651648f2c54688f9262da72a075b61fd247be"
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end
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head do
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url "https://github.com/ncbi/sra-tools.git", branch: "master"
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resource "ncbi-vdb" do
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url "https://github.com/ncbi/ncbi-vdb.git", branch: "master"
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end
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end
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depends_on "cmake" => :build
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depends_on "hdf5"
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depends_on macos: :catalina
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uses_from_macos "libxml2"
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def install
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(buildpath/"ncbi-vdb-source").install resource("ncbi-vdb")
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# Workaround to allow clang/aarch64 build to use the gcc/arm64 directory
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# Issue ref: https://github.com/ncbi/ncbi-vdb/issues/65
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ln_s "../gcc/arm64", buildpath/"ncbi-vdb-source/interfaces/cc/clang/arm64" if Hardware::CPU.arm?
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# Need to use HDF 1.10 API: error: too few arguments to function call, expected 5, have 4
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# herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5P_DEFAULT );
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ENV.append_to_cflags "-DH5_USE_110_API"
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system "cmake", "-S", "ncbi-vdb-source", "-B", "ncbi-vdb-build", *std_cmake_args,
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"-DNGS_INCDIR=#{buildpath}/ngs/ngs-sdk"
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system "cmake", "--build", "ncbi-vdb-build"
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system "cmake", "-S", ".", "-B", "sra-tools-build", *std_cmake_args,
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"-DVDB_BINDIR=#{buildpath}/ncbi-vdb-build",
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"-DVDB_LIBDIR=#{buildpath}/ncbi-vdb-build/lib",
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"-DVDB_INCDIR=#{buildpath}/ncbi-vdb-source/interfaces"
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system "cmake", "--build", "sra-tools-build"
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system "cmake", "--install", "sra-tools-build"
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# Remove non-executable files.
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(bin/"ncbi").rmtree
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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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