busco: create config.ini

Closes brewsci#642.

Signed-off-by: Gabriel Leventhal <[email protected]>

Formula/busco.rb

@@ -5,7 +5,7 @@ class Busco < Formula
   homepage "https://busco.ezlab.org"
   url "https://gitlab.com/ezlab/busco/repository/3.0.2/archive.tar.bz2"
   sha256 "cd0699545a126c7cc94604eef7c8dc50379b5d11becbad3a0f55d995a4c5e1c0"
-  revision 1
+  revision 2
   head "https://gitlab.com/ezlab/busco.git"
 
   bottle do
@@ -15,17 +15,57 @@ class Busco < Formula
     sha256 "f77caa27c9ea8e866682a00cd93bbb626f6139b6a95e1c7354b0268ad806a253" => :x86_64_linux
   end
 
+  depends_on "augustus"
+  depends_on "blast"
+  depends_on "hmmer"
   depends_on "python"
-  depends_on "blast" => :recommended
-  # Also depends on augustus and hmmer
 
   def install
     inreplace Dir["scripts/*.py"], "#!/usr/bin/env python", "#!#{HOMEBREW_PREFIX}/bin/python3"
     system "python3", "setup.py", "install", "--prefix=#{prefix}"
-    bin.install Dir["scripts/*"]
-    bin.install_symlink "run_BUSCO.py" => "busco"
+
+    libexec.install Dir["scripts/*"]
+    (bin/"busco").write_env_script(libexec/"run_BUSCO.py", :AUGUSTUS_CONFIG_PATH => "#{Formula["augustus"].prefix}/config/")
+
     doc.install "BUSCO_v3_userguide.pdf"
-    prefix.install "config/config.ini.default"
+    prefix.install "config"
+
+    (prefix/"config/config.ini").write <<~EOS
+      [busco]
+      [tblastn]
+      path = #{Formula["blast"].bin}
+      [makeblastdb]
+      path = #{Formula["blast"].bin}
+      [augustus]
+      path = #{Formula["augustus"].bin}
+      [etraining]
+      path = #{Formula["augustus"].bin}
+      [gff2gbSmallDNA.pl]
+      path = #{Formula["augustus"].prefix}/scripts/
+      [new_species.pl]
+      path = #{Formula["augustus"].prefix}/scripts/
+      [optimize_augustus.pl]
+      path = #{Formula["augustus"].prefix}/scripts/
+      [hmmsearch]
+      path = #{Formula["hmmer"].bin}
+      [Rscript]
+      path = #{HOMEBREW_PREFIX}/bin
+    EOS
+  end
+
+  def caveats; <<~EOS
+    You probably also want to download lineage datasets to run BUSCO:
+
+      https://busco.ezlab.org
+
+    To generate graphs, also make sure a working R is installed:
+
+      brew cask install r
+
+    or alternatively
+
+      brew install r
+  EOS
   end
 
   test do