75 lines
2.5 KiB
Ruby
75 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/2.8.2-5.tar.gz"
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version "2.8.2-5"
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sha256 "15b41420d95a72de9e24dec53401cc10e435a17ee9c5eec45ef78fd078db544c"
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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 "dd18ab4cc9d449dbbe79d22c1ad196b596439f1efe8d0617d8c261d9b5c82f7b" => :high_sierra
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sha256 "114f14b37c07ed9ee179fd75f5d5093a73e35d5edc9b2923305af59a45033a4c" => :sierra
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sha256 "7d46ae4e277640e7bc956caa37a95b7f7e4decfc826ef6b42f870683972dc855" => :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/1.3.0.tar.gz"
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sha256 "803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2"
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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/2.8.2-2.tar.gz"
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version "2.8.2-2"
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sha256 "7866f7abf00e35faaa58eb3cdc14785e6d42bde515de4bb3388757eb0c8f3c95"
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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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