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-rw-r--r--var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch (renamed from var/spack/repos/builtin/packages/bowtie2/bowtie2-2.5.patch)0
-rw-r--r--var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch16
-rw-r--r--var/spack/repos/builtin/packages/bowtie2/package.py16
3 files changed, 28 insertions, 4 deletions
diff --git a/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.5.patch b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch
index 290be39c73..290be39c73 100644
--- a/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.5.patch
+++ b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch
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/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()