01/01: gnu: bowtie: fix build errors

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 241e122193e6eee900cab1f3a1caec2f90603560
Author: Ricardo Wurmus <address@hidden>
Date:   Thu Jan 29 10:35:52 2015 +0100

    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.
---
 gnu-system.am                                  |    1 +
 gnu/packages/bioinformatics.scm                |    6 +++-
 gnu/packages/patches/bowtie-fix-makefile.patch |   31 ++++++++++++++++++++++++
 3 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/gnu-system.am b/gnu-system.am
index 6c2d66b..1211855 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 ff6c337..620c809 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 <address@hidden>
+;;; Copyright © 2014, 2015 Ricardo Wurmus <address@hidden>
 ;;;
 ;;; 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 0000000..5ac6573
--- /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 <address@hidden>
+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