From 13eb461ec31520c75d6d604038e455468d061a61 Mon Sep 17 00:00:00 2001
From: Mario Melara <mamelara@genepool1.nersc.gov>
Date: Thu, 24 Sep 2015 11:21:54 -0700
Subject: Adding bowtie2 package along with patch

---
 var/spack/packages/bowtie2/bowtie2-2.5.patch | 16 ++++++++++++++++
 var/spack/packages/bowtie2/package.py        | 24 ++++++++++++++++++++++++
 2 files changed, 40 insertions(+)
 create mode 100644 var/spack/packages/bowtie2/bowtie2-2.5.patch
 create mode 100644 var/spack/packages/bowtie2/package.py

(limited to 'var')

diff --git a/var/spack/packages/bowtie2/bowtie2-2.5.patch b/var/spack/packages/bowtie2/bowtie2-2.5.patch
new file mode 100644
index 0000000000..290be39c73
--- /dev/null
+++ b/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
diff --git a/var/spack/packages/bowtie2/package.py b/var/spack/packages/bowtie2/package.py
new file mode 100644
index 0000000000..339aab6598
--- /dev/null
+++ b/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)
+
-- 
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