From 9385659aa1d692f2fce9b38d90156e332b2bf48f Mon Sep 17 00:00:00 2001
From: George Hartzell <hartzell@alerce.com>
Date: Tue, 28 Mar 2017 19:35:46 -0700
Subject: bowtie2: add support for version 2.3.1 (#3599)

* Add support for 2.3.1

Updated digest and added a dependency on tbb.

* Cleanup patch name and add description
---
 .../repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch   | 16 ++++++++++++++++
 .../repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch   | 16 ++++++++++++++++
 .../repos/builtin/packages/bowtie2/bowtie2-2.5.patch     | 16 ----------------
 var/spack/repos/builtin/packages/bowtie2/package.py      | 16 ++++++++++++----
 4 files changed, 44 insertions(+), 20 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch
 create mode 100644 var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch
 delete mode 100644 var/spack/repos/builtin/packages/bowtie2/bowtie2-2.5.patch

diff --git a/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch
new file mode 100644
index 0000000000..290be39c73
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.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/repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch
new file mode 100644
index 0000000000..0f4a15b1a1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch
@@ -0,0 +1,16 @@
+--- Makefile.orig	2017-03-24 20:43:00.304532976 -0700
++++ Makefile	2017-03-24 20:48:59.644532037 -0700
+@@ -26,10 +26,10 @@
+
+ INC =
+ LIBS = -lreadline -ltermcap -lz
+-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/repos/builtin/packages/bowtie2/bowtie2-2.5.patch b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.5.patch
deleted file mode 100644
index 290be39c73..0000000000
--- a/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.5.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- 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/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py
index a8a1a34ed4..6dbcea8dd0 100644
--- a/var/spack/repos/builtin/packages/bowtie2/package.py
+++ b/var/spack/repos/builtin/packages/bowtie2/package.py
@@ -27,12 +27,20 @@ from glob import glob
 
 
 class Bowtie2(Package):
-    """Description"""
+    """Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+       sequencing reads to long reference sequences"""
     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")
+    version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478')
+    version('2.2.5', '51fa97a862d248d7ee660efc1147c75f')
 
-    patch('bowtie2-2.5.patch', when='@2.2.5', level=0)
+    depends_on('tbb', when='@2.3.1')
+
+    patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
+    patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
+
+    def url_for_version(self, version):
+        url="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/{0}/bowtie2-{0}-source.zip"
+        return url.format(version)
 
     def install(self, spec, prefix):
         make()
-- 
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