75 lines
2.5 KiB
Ruby
75 lines
2.5 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/2.10.0.tar.gz"
|
|
sha256 "6d2b02bad674cde6b9677a522f62da092da5471d23738976abce8eae5710fa0c"
|
|
head "https://github.com/ncbi/sra-tools.git"
|
|
|
|
bottle do
|
|
cellar :any_skip_relocation
|
|
sha256 "5666b45a693e675a145503ee348aa9be199b6dd53d8e3582e6a2af2f4f647b94" => :catalina
|
|
sha256 "8d9a22d8cc446e66d66b44e8d8e2bbdf60faaa9cc8166e9c7cad1dd5e98abf8b" => :mojave
|
|
sha256 "3dc2db39ac207dc8ba786ba808105cba4128cc9cb5573a02c28e9a71208886c9" => :high_sierra
|
|
end
|
|
|
|
depends_on "hdf5"
|
|
depends_on "libmagic"
|
|
uses_from_macos "libxml2"
|
|
uses_from_macos "perl"
|
|
|
|
resource "ngs-sdk" do
|
|
url "https://github.com/ncbi/ngs/archive/2.10.0.tar.gz"
|
|
sha256 "4139adff83af213d7880bc80d1c0f5ee9b00c6c4e615d00aa47aaa267e40ed25"
|
|
end
|
|
|
|
resource "ncbi-vdb" do
|
|
url "https://github.com/ncbi/ncbi-vdb/archive/2.10.0.tar.gz"
|
|
sha256 "a6cc88e8d12f536dc96d5f60698d0ef4cf2f63e31d3d12d23da39b1de39563e1"
|
|
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
|