diff --git a/gnu-system.am b/gnu-system.am
index 6c2d66bbda4235ef6359133d2df7c78380e2035d..1211855f5484f94375a6074d3954e1c8a1ce0a09 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -346,6 +346,7 @@ dist_patch_DATA = \
gnu/packages/patches/automake-skip-amhello-tests.patch \
gnu/packages/patches/avahi-localstatedir.patch \
gnu/packages/patches/avrdude-fix-libusb.patch \
+ gnu/packages/patches/bowtie-fix-makefile.patch \
gnu/packages/patches/bigloo-gc-shebangs.patch \
gnu/packages/patches/binutils-ld-new-dtags.patch \
gnu/packages/patches/binutils-loongson-workaround.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ff6c3379af8d52d35ef43f4a72bebd8e090c825b..620c8090b7c1a12648bc576742ee06085dda2cd9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -95,7 +95,8 @@ (define-public bowtie
(("^CPP = .*$") "CPP = g++")
;; replace BUILD_HOST and BUILD_TIME for deterministic build
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
- (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
+ (patches (list (search-patch "bowtie-fix-makefile.patch")))))
(build-system gnu-build-system)
(inputs `(("perl" ,perl)
("perl-clone" ,perl-clone)
@@ -133,6 +134,7 @@ (define-public bowtie
genome with an FM Index to keep its memory footprint small: for the human
genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
gapped, local, and paired-end alignment modes.")
+ (supported-systems '("x86_64-linux"))
(license license:gpl3+)))
(define-public samtools
diff --git a/gnu/packages/patches/bowtie-fix-makefile.patch b/gnu/packages/patches/bowtie-fix-makefile.patch
new file mode 100644
index 0000000000000000000000000000000000000000..5ac65731cbedd23aa9d5651acc0a599d61ebe100
--- /dev/null
+++ b/gnu/packages/patches/bowtie-fix-makefile.patch
@@ -0,0 +1,31 @@
+From 4a99b0023bdfbbe486b9649489a32ea184c18c9a Mon Sep 17 00:00:00 2001
+From: Valentin Antonescu <valentin@jhu.edu>
+Date: Tue, 2 Dec 2014 11:19:13 -0500
+Subject: [PATCH] Make sure the Mavericks test happens only under Darwin.
+
+---
+ Makefile | 11 +++++------
+ 1 file changed, 5 insertions(+), 6 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index d74f7c8..a4cdfa7 100644
+--- a/Makefile
++++ b/Makefile
+@@ -54,12 +54,11 @@ endif
+ MACOS = 0
+ ifneq (,$(findstring Darwin,$(shell uname)))
+ MACOS = 1
+-endif
+-
+-ifneq (,$(findstring 13,$(shell uname -r)))
+- CPP = clang++
+- CC = clang
+- EXTRA_FLAGS += -stdlib=libstdc++
++ ifneq (,$(findstring 13,$(shell uname -r)))
++ CPP = clang++
++ CC = clang
++ EXTRA_FLAGS += -stdlib=libstdc++
++ endif
+ endif
+
+ POPCNT_CAPABILITY ?= 1