cufflinks 2.0.2

- Upgrade cufflinks to version 2.0.2
- Add a dep on eigen. It won't build without it.
- Make all the deps `:build` for the same reason.
- It still fails with clang, but llvm is okay.
- Add an env var, `EIGEN_CPPFLAGS` to help it find eigen.
- Add to `LDFLAGS` an `-lboost_system-mt` fixes missing symbols
- Run sed on 120 files to fix a boost::FOREACH issue.
- Note in the comments the source of the sed fix.
- Specify `--mandir` even though no man pages at this time.
- Run `make` in parallel.  Run the install as a j1.
- Works well with superenv

Fixes Homebrew#14385

Library/Formula/cufflinks.rb

@@ -1,21 +1,32 @@
 require 'formula'
 
 class Cufflinks < Formula
-  url 'http://cufflinks.cbcb.umd.edu/downloads/cufflinks-1.3.0.tar.gz'
   homepage 'http://cufflinks.cbcb.umd.edu/'
-  sha1 'fa93a7a33f0649793ec1d185cb7043fd0dc2018b'
+  url 'http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.0.2.tar.gz'
+  sha1 '91954b4945c49ca133b39bffadf51bdf9ec2ff26'
 
-  depends_on 'boost'
-  depends_on 'samtools'
+  depends_on 'boost'    => :build
+  depends_on 'samtools' => :build
+  depends_on 'eigen'    => :build
 
   fails_with :clang do
     build 421
   end
 
   def install
-    ENV.deparallelize
+    ENV['EIGEN_CPPFLAGS'] = '-I'+Formula.factory('eigen').include/'eigen3'
+    ENV.append 'LDFLAGS', '-lboost_system-mt'
+    cd 'src' do
+      # Fixes 120 files redefining `foreach` that break building with boost
+      # See http://seqanswers.com/forums/showthread.php?t=16637
+      `for x in *.cpp *.h; do sed 's/foreach/for_each/' $x > x; mv x $x; done`
+      inreplace 'common.h', 'for_each.hpp', 'foreach.hpp'
+    end
     system "./configure", "--disable-debug", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make install"
+                          "--prefix=#{prefix}",
+                          "--mandir=#{man}"
+    system 'make'
+    ENV.j1
+    system 'make install'
   end
 end