biopieces 2291: New formula

The Biopieces are a collection of bioinformatics tools that can be
pieced together in a very easy and flexible manner to perform both
simple and complex tasks.

biopieces.rb

@@ -0,0 +1,58 @@
+require "formula"
+
+class Biopieces < Formula
+  homepage "https://code.google.com/p/biopieces/"
+  version '2291'
+  url "http://biopieces.googlecode.com/svn/trunk/", :revision => version
+  head "http://biopieces.googlecode.com/svn/trunk/"
+
+  depends_on "biopieces" => :ruby
+
+  depends_on "Bit::Vector" => :perl
+  depends_on "Carp::Clan" => :perl
+  depends_on "Class::Inspector" => :perl
+  depends_on "DBI" => :perl
+  depends_on "DB_File" => :perl
+  depends_on "HTML::Parser" => :perl
+  depends_on "Inline" => :perl
+  depends_on "LWP" => :perl
+  depends_on "Module::Build" => :perl
+  depends_on "Parse::RecDescent" => :perl
+  depends_on "SOAP::Lite" => :perl
+  depends_on "SVG" => :perl
+  depends_on "Term::ReadKey" => :perl
+  depends_on "Time::HiRes" => :perl
+  depends_on "URI" => :perl
+  depends_on "XML::Parser" => :perl
+  depends_on "version" => :perl
+
+  def install
+    prefix.install Dir['*']
+    bin.mkdir
+    cd bin do
+      bin.install_symlink Dir['../bp_bin/*']
+    end
+    rm_f bin/'00README'
+
+    # Install the documentation.
+    cd prefix do
+      system 'svn checkout http://biopieces.googlecode.com/svn/wiki bp_usage'
+    end
+  end
+
+  def caveats; <<-EOS.undent
+      To use Biopieces, set the following environment variables:
+        export BP_DIR=#{opt_prefix}
+        export BP_DATA="$BP_DIR/bp_data"
+        export BP_LOG=~/Library/Logs/Biopieces
+        export BP_TMP=/tmp
+        export PERL5LIB="$BP_DIR/code_perl:$PERL5LIB"
+        export RUBYLIB="$BP_DIR/code_ruby/lib:$RUBYLIB"
+        mkdir -p $BP_LOG
+    EOS
+  end
+
+  test do
+    system "#{bin}/read_fasta --help"
+  end
+end