46 lines
2.0 KiB
Ruby
46 lines
2.0 KiB
Ruby
class Bbtools < Formula
|
|
desc "Brian Bushnell's tools for manipulating reads"
|
|
homepage "https://jgi.doe.gov/data-and-tools/bbtools/"
|
|
url "https://downloads.sourceforge.net/bbmap/BBMap_38.99.tar.gz"
|
|
sha256 "7a9934abe0e678fda74d5d6c5d83d489dbd0b5ad1fca3055e37ba9dac2bfc1bb"
|
|
license "BSD-3-Clause"
|
|
|
|
bottle do
|
|
sha256 cellar: :any, arm64_monterey: "eb5b06b552ebb6d629173fccc1edf71f9acf76df31b72a6c58d33f7b87deba0b"
|
|
sha256 cellar: :any, arm64_big_sur: "eafbde7dfefd35d93b8293034f4148766c44f122d5dd972ad65c79aeacb088e1"
|
|
sha256 cellar: :any, monterey: "15186c2f1b5056000c57a26abd92a57750e95a724e7cde82c2b5684c544f6267"
|
|
sha256 cellar: :any, big_sur: "91454839e82d4223153b97a1536d3931b2eebf2125541f7123c98c057af067b4"
|
|
sha256 cellar: :any, catalina: "0ee4598f3a27d5bb1fb8cfe2ea68b31a57e4d48ddbdf2909b72e1486f6fe6002"
|
|
sha256 cellar: :any_skip_relocation, x86_64_linux: "5766c254237c4b387fa3aee3d682773ef458eca3d342ca8d34a7246a42b9ee02"
|
|
end
|
|
|
|
depends_on "openjdk"
|
|
|
|
def install
|
|
cd "jni" do
|
|
rm Dir["libbbtoolsjni.*", "*.o"]
|
|
system "make", "-f", OS.mac? ? "makefile.osx" : "makefile.linux"
|
|
end
|
|
libexec.install %w[current jni resources]
|
|
libexec.install Dir["*.sh"]
|
|
bin.install Dir[libexec/"*.sh"]
|
|
bin.env_script_all_files(libexec, Language::Java.overridable_java_home_env)
|
|
doc.install Dir["docs/*"]
|
|
end
|
|
|
|
test do
|
|
res = libexec/"resources"
|
|
args = %W[in=#{res}/sample1.fq.gz
|
|
in2=#{res}/sample2.fq.gz
|
|
out=R1.fastq.gz
|
|
out2=R2.fastq.gz
|
|
ref=#{res}/phix174_ill.ref.fa.gz
|
|
k=31
|
|
hdist=1]
|
|
system "#{bin}/bbduk.sh", *args
|
|
assert_match "bbushnell@lbl.gov", shell_output("#{bin}/bbmap.sh")
|
|
assert_match "maqb", shell_output("#{bin}/bbmap.sh --help 2>&1")
|
|
assert_match "minkmerhits", shell_output("#{bin}/bbduk.sh --help 2>&1")
|
|
end
|
|
end
|