augustus: fix bug in proteinprofile on macOS

Closes #40220.

Signed-off-by: Shaun Jackman <sjackman@gmail.com>

Formula/augustus.rb

@@ -3,6 +3,7 @@ class Augustus < Formula
   homepage "http://bioinf.uni-greifswald.de/augustus/"
   url "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.2.tar.gz"
   sha256 "989a95fe3a83d62af4d323a9727d11b2c566adcf4d789d5d86d7b842d83e7671"
+  head "https://github.com/Gaius-Augustus/Augustus.git"
 
   bottle do
     sha256 "2d7449f08dbf38ee7a46d51e2f17032221b0567e4a215e7d309602cee8724ce5" => :mojave
@@ -10,8 +11,9 @@ class Augustus < Formula
     sha256 "020e9e8531aeaad48d06a96ca78eda64eae25e3737e69941f9069e6abd4e898d" => :sierra
   end
 
+  depends_on "boost" => :build
   depends_on "bamtools"
-  depends_on "boost"
+  depends_on "gcc"
 
   def install
     # Avoid "fatal error: 'sam.h' file not found" by not building bam2wig
@@ -30,10 +32,20 @@ class Augustus < Formula
 
     # Compile executables for macOS. Tarball ships with executables for Linux.
     system "make", "clean"
-    system "make"
 
+    # Clang breaks proteinprofile on macOS. This issue has been first reported
+    # to upstream in 2016 (see https://github.com/nextgenusfs/funannotate/issues/3).
+    # See also https://github.com/Gaius-Augustus/Augustus/issues/64
+    cd "src" do
+      with_env("HOMEBREW_CC" => "gcc-9") do
+        system "make"
+      end
+    end
+
+    system "make"
     system "make", "install", "INSTALLDIR=#{prefix}"
     bin.env_script_all_files libexec/"bin", :AUGUSTUS_CONFIG_PATH => prefix/"config"
+    pkgshare.install "examples"
   end
 
   test do
@@ -43,5 +55,10 @@ class Augustus < Formula
     EOS
     cmd = "#{bin}/augustus --species=human test.fasta"
     assert_match "Predicted genes", shell_output(cmd)
+
+    cp pkgshare/"examples/example.fa", testpath
+    cp pkgshare/"examples/profile/HsDHC.prfl", testpath
+    cmd = "#{bin}/augustus --species=human --proteinprofile=HsDHC.prfl example.fa 2> /dev/null"
+    assert_match "HS04636	AUGUSTUS	gene	966	6903	1	+	.	g1", shell_output(cmd)
   end
 end