72 lines
2.4 KiB
Ruby
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/2.9.1.tar.gz"
|
|
sha256 "61f35be7e26cb538a93b8e7e0afd6bc593e97333638dc0de176a6a828b9b504e"
|
|
head "https://github.com/ncbi/sra-tools.git"
|
|
|
|
bottle do
|
|
cellar :any
|
|
sha256 "b633b23da5cceda972e54edad82310b51cea5974cfa254d9f472d73ab32ea103" => :high_sierra
|
|
sha256 "bf01cf629dfff991ea0120ba71b223aff9d2b06e554fda2fb0ea086f0cda58fd" => :sierra
|
|
sha256 "db7fd18c4521d867a0e92ae48ae32b4abed0e80ae39c7b14368775166bb73a27" => :el_capitan
|
|
end
|
|
|
|
depends_on "hdf5"
|
|
depends_on "libmagic"
|
|
|
|
resource "ngs-sdk" do
|
|
url "https://github.com/ncbi/ngs/archive/2.9.1.tar.gz"
|
|
sha256 "c24c93bd70ed198a44c6b9dba0d6704edc90f228f832f2fef21fa5342303fc50"
|
|
end
|
|
|
|
resource "ncbi-vdb" do
|
|
url "https://github.com/ncbi/ncbi-vdb/archive/2.9.1.tar.gz"
|
|
sha256 "ef55c5dac0e9f0f05cfff6c9e56061b72aa034153895990bf2b7daaba8f06739"
|
|
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
|