[PATCH]: gnu: bowtie: only support x86_64-linux

[PATCH]: gnu: bowtie: only support x86_64-linux

[Ricardo Wurmus]

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Since bowtie's Makefile explicitly checks that the system it is built on
is x86_64 building on MIPS and i686 should be disabled.  (See bug#19708
for discussion.)

This is what the attached patch does.

~~ Ricardo


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From 9789efe14b8cf00ebf6b39a63146483fbe220535 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 29 Jan 2015 10:35:52 +0100
Subject: [PATCH] gnu: bowtie: only x86_64 is supported.

* gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field.
---
 gnu/packages/bioinformatics.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ff6c337..3ea82ba 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -133,6 +133,7 @@ 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
-- 
1.9.3

Re: [PATCH]: gnu: bowtie: only support x86_64-linux

[Ricardo Wurmus]

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Ricardo Wurmus writes:

> Since bowtie's Makefile explicitly checks that the system it is built on
> is x86_64 building on MIPS and i686 should be disabled.  (See bug#19708
> for discussion.)
>
> This is what the attached patch does.

Please disregard the above patch and consider the attached one instead,
which also patches the Makefile (with an upstream patch for the next
release) to fix the build errors on x86_64.

~~ Ricardo


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From cdabe548b67185e0c652ebacc90f95cfeffc5888 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 29 Jan 2015 10:35:52 +0100
Subject: [PATCH] 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 (MODULES): 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(-)
 create mode 100644 gnu/packages/patches/bowtie-fix-makefile.patch

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 <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 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 <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
-- 
1.9.3

Re: [PATCH]: gnu: bowtie: only support x86_64-linux

[Ricardo Wurmus]

> Please disregard the above patch and consider the attached one instead,
> which also patches the Makefile (with an upstream patch for the next
> release) to fix the build errors on x86_64.

The ChangeLog should be this instead, of course (dist_patch_DATA instead
of MODULES):

    * 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.

Sorry for the noise.

Re: [PATCH]: gnu: bowtie: only support x86_64-linux

[Mark H Weaver]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

>> Please disregard the above patch and consider the attached one instead,
>> which also patches the Makefile (with an upstream patch for the next
>> release) to fix the build errors on x86_64.
>
> The ChangeLog should be this instead, of course (dist_patch_DATA instead
> of MODULES):
>
>     * 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.

Looks good to me.  Okay to push!

    Thanks!
      Mark