From 6f0ba3f37d9d6d328fd4d37dbb6f512ee2233497 Mon Sep 17 00:00:00 2001
From: Shaun Jackman <sjackman@gmail.com>
Date: Sun, 7 Jan 2018 18:10:36 -0800
Subject: [PATCH] bioawk: import from homebrew/science

Closes #22544.

Signed-off-by: ilovezfs <ilovezfs@icloud.com>
---
 Formula/bioawk.rb | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 Formula/bioawk.rb

diff --git a/Formula/bioawk.rb b/Formula/bioawk.rb
new file mode 100644
index 00000000000..497a2c02cf7
--- /dev/null
+++ b/Formula/bioawk.rb
@@ -0,0 +1,25 @@
+class Bioawk < Formula
+  desc "AWK modified for biological data"
+  homepage "https://github.com/lh3/bioawk"
+  url "https://github.com/lh3/bioawk/archive/v1.0.tar.gz"
+  sha256 "5cbef3f39b085daba45510ff450afcf943cfdfdd483a546c8a509d3075ff51b5"
+
+  def install
+    # Fix make: *** No rule to make target `ytab.h', needed by `b.o'.
+    ENV.deparallelize
+
+    system "make"
+    bin.install "bioawk"
+    man1.install "awk.1" => "bioawk.1"
+  end
+
+  test do
+    (testpath/"test.fasta").write <<~EOS
+      >U00096.2:1-70
+      AGCTTTTCATTCTGACTGCAACGGGCAATATGTCT
+      CTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
+    EOS
+    cmd = "#{bin}/bioawk -cfastx '{print length($seq)}' test.fasta"
+    assert_equal "70", shell_output(cmd).chomp
+  end
+end