summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-01-29 10:35:52 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-01-30 10:45:27 +0100
commit241e122193e6eee900cab1f3a1caec2f90603560 (patch)
tree728f0046a3d103ea7abd9739bc16b2326d68b190
parente89fa047f76048ac907756a5f08ddc06c84c6c40 (diff)
downloadpatches-241e122193e6eee900cab1f3a1caec2f90603560.tar
patches-241e122193e6eee900cab1f3a1caec2f90603560.tar.gz
gnu: bowtie: fix build errors
* gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field and add Makefile patch. * gnu/packages/patches/bowtie-fix-makefile.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
-rw-r--r--gnu-system.am1
-rw-r--r--gnu/packages/bioinformatics.scm6
-rw-r--r--gnu/packages/patches/bowtie-fix-makefile.patch31
3 files changed, 36 insertions, 2 deletions
diff --git a/gnu-system.am b/gnu-system.am
index 6c2d66bbda..1211855f54 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 ff6c3379af..620c8090b7 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 @@ BED, GFF/GTF, VCF.")
(("^CPP = .*$") "CPP = g++")
;; replace BUILD_HOST and BUILD_TIME for deterministic build
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
- (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
+ (patches (list (search-patch "bowtie-fix-makefile.patch")))))
(build-system gnu-build-system)
(inputs `(("perl" ,perl)
("perl-clone" ,perl-clone)
@@ -133,6 +134,7 @@ aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
genome with an FM Index to keep its memory footprint small: for the human
genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
gapped, local, and paired-end alignment modes.")
+ (supported-systems '("x86_64-linux"))
(license license:gpl3+)))
(define-public samtools
diff --git a/gnu/packages/patches/bowtie-fix-makefile.patch b/gnu/packages/patches/bowtie-fix-makefile.patch
new file mode 100644
index 0000000000..5ac65731cb
--- /dev/null
+++ b/gnu/packages/patches/bowtie-fix-makefile.patch
@@ -0,0 +1,31 @@
+From 4a99b0023bdfbbe486b9649489a32ea184c18c9a Mon Sep 17 00:00:00 2001
+From: Valentin Antonescu <valentin@jhu.edu>
+Date: Tue, 2 Dec 2014 11:19:13 -0500
+Subject: [PATCH] Make sure the Mavericks test happens only under Darwin.
+
+---
+ Makefile | 11 +++++------
+ 1 file changed, 5 insertions(+), 6 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index d74f7c8..a4cdfa7 100644
+--- a/Makefile
++++ b/Makefile
+@@ -54,12 +54,11 @@ endif
+ MACOS = 0
+ ifneq (,$(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