Adding bowtie2 package along with patch

var/spack/packages/bowtie2/bowtie2-2.5.patch

@@ -0,0 +1,16 @@
+--- Makefile	2015-02-26 10:50:00.000000000 -0800
++++ Makefile.new	2015-07-29 18:03:59.891357399 -0700
+@@ -22,10 +22,10 @@
+ #
+ 
+ INC =
+-GCC_PREFIX = $(shell dirname `which gcc`)
++GCC_PREFIX =
+ GCC_SUFFIX =
+-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
++CC = cc 
++CPP = c++
+ CXX = $(CPP)
+ HEADERS = $(wildcard *.h)
+ BOWTIE_MM = 1

var/spack/packages/bowtie2/package.py

@@ -0,0 +1,24 @@
+from spack import *
+from glob import glob
+class Bowtie2(Package):
+    """Description"""
+    homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
+    version('2.2.5','51fa97a862d248d7ee660efc1147c75f', url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip")
+
+    patch('bowtie2-2.5.patch',when='@2.2.5', level=0)
+
+    def install(self, spec, prefix):
+        make()
+        mkdirp(prefix.bin)
+        for bow in glob("bowtie2*"):
+            install(bow, prefix.bin)
+        # install('bowtie2',prefix.bin)
+        # install('bowtie2-align-l',prefix.bin)
+        # install('bowtie2-align-s',prefix.bin)
+        # install('bowtie2-build',prefix.bin)
+        # install('bowtie2-build-l',prefix.bin)
+        # install('bowtie2-build-s',prefix.bin)
+        # install('bowtie2-inspect',prefix.bin)
+        # install('bowtie2-inspect-l',prefix.bin)
+        # install('bowtie2-inspect-s',prefix.bin)
+