homebrew-core/Formula/sratoolkit.rb
2018-02-25 12:59:28 +10:00

72 lines
2.4 KiB
Ruby

class Sratoolkit < Formula
desc "Data tools for INSDC Sequence Read Archive"
homepage "https://github.com/ncbi/sra-tools"
url "https://github.com/ncbi/sra-tools/archive/2.9.0.tar.gz"
sha256 "fbdbbf69cf95afca311b9759e14a991dafcb95549ffd5e2e21fb0ecc99fa06aa"
head "https://github.com/ncbi/sra-tools.git"
bottle do
cellar :any
sha256 "c7f266cafb38da2d4a97f7dd55495bffaee1b4de10dabfff0cd2169feb294c92" => :high_sierra
sha256 "77c82b91cc83271178381d0787d7f0242cb56c44119c9e07426c25dea7a2e689" => :sierra
sha256 "3ce0a6f82a5b18b891adac99f1fedf1a941e54356989d8e076bbe7df17b62dc0" => :el_capitan
end
depends_on "hdf5"
depends_on "libmagic"
resource "ngs-sdk" do
url "https://github.com/ncbi/ngs/archive/2.9.0.tar.gz"
sha256 "7e4f9e4490309b6fb33ec9370e5202ad446b10b75c323ba8226c29ca364a0857"
end
resource "ncbi-vdb" do
url "https://github.com/ncbi/ncbi-vdb/archive/2.9.0.tar.gz"
sha256 "40fdd0a34592f76bdad174d3c2b57b3efcd1e2240512a383bd6e6263b33a6146"
end
def install
ngs_sdk_prefix = buildpath/"ngs-sdk-prefix"
resource("ngs-sdk").stage do
cd "ngs-sdk" do
system "./configure",
"--prefix=#{ngs_sdk_prefix}",
"--build=#{buildpath}/ngs-sdk-build"
system "make"
system "make", "install"
end
end
ncbi_vdb_source = buildpath/"ncbi-vdb-source"
ncbi_vdb_build = buildpath/"ncbi-vdb-build"
ncbi_vdb_source.install resource("ncbi-vdb")
cd ncbi_vdb_source do
system "./configure",
"--prefix=#{buildpath/"ncbi-vdb-prefix"}",
"--with-ngs-sdk-prefix=#{ngs_sdk_prefix}",
"--build=#{ncbi_vdb_build}"
ENV.deparallelize { system "make" }
end
# Fix the error: ld: library not found for -lmagic-static
# Upstream PR: https://github.com/ncbi/sra-tools/pull/105
inreplace "tools/copycat/Makefile", "-smagic-static", "-smagic"
system "./configure",
"--prefix=#{prefix}",
"--with-ngs-sdk-prefix=#{ngs_sdk_prefix}",
"--with-ncbi-vdb-sources=#{ncbi_vdb_source}",
"--with-ncbi-vdb-build=#{ncbi_vdb_build}",
"--build=#{buildpath}/sra-tools-build"
system "make", "install"
# Remove non-executable files.
rm_r [bin/"magic", bin/"ncbi"]
end
test do
assert_match "Read 1 spots for SRR000001", shell_output("#{bin}/fastq-dump -N 1 -X 1 SRR000001")
assert_match "@SRR000001.1 EM7LVYS02FOYNU length=284", File.read("SRR000001.fastq")
end
end