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-rw-r--r--gnu-system.am1
-rw-r--r--gnu/packages/bioinformatics.scm38
-rw-r--r--gnu/packages/patches/bowtie-fix-makefile.patch31
3 files changed, 16 insertions, 54 deletions
diff --git a/gnu-system.am b/gnu-system.am
index fa2f038402..dc2631bae1 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -416,7 +416,6 @@ dist_patch_DATA = \
gnu/packages/patches/avidemux-install-to-lib.patch \
gnu/packages/patches/avrdude-fix-libusb.patch \
gnu/packages/patches/bash-completion-directories.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 a0b7864918..50e1ce714e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
@@ -603,7 +603,7 @@ errors at the end of reads.")
(define-public bowtie
(package
(name "bowtie")
- (version "2.2.4")
+ (version "2.2.6")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
@@ -611,42 +611,36 @@ errors at the end of reads.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
+ "1ssfvymxfrap6f9pf86s9bvsbqdgka4abr2r7j3mgr4w1l289m86"))
(modules '((guix build utils)))
(snippet
'(substitute* "Makefile"
- (("^CC = .*$") "CC = gcc")
- (("^CPP = .*$") "CPP = g++")
;; replace BUILD_HOST and BUILD_TIME for deterministic build
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
- (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
- (patches (list (search-patch "bowtie-fix-makefile.patch")))))
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
(build-system gnu-build-system)
(inputs `(("perl" ,perl)
("perl-clone" ,perl-clone)
("perl-test-deep" ,perl-test-deep)
("perl-test-simple" ,perl-test-simple)
- ("python" ,python-2)))
+ ("python" ,python-2)
+ ("tbb" ,tbb)))
(arguments
- '(#:make-flags '("allall")
+ '(#:make-flags
+ (list "allall"
+ "WITH_TBB=1"
+ (string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(alist-delete
'configure
(alist-replace
- 'install
+ 'check
(lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (for-each (lambda (file)
- (install-file file bin))
- (find-files "." "bowtie2.*"))))
- (alist-replace
- 'check
- (lambda* (#:key outputs #:allow-other-keys)
- (system* "perl"
- "scripts/test/simple_tests.pl"
- "--bowtie2=./bowtie2"
- "--bowtie2-build=./bowtie2-build"))
- %standard-phases)))))
+ (system* "perl"
+ "scripts/test/simple_tests.pl"
+ "--bowtie2=./bowtie2"
+ "--bowtie2-build=./bowtie2-build"))
+ %standard-phases))))
(home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
(synopsis "Fast and sensitive nucleotide sequence read aligner")
(description
diff --git a/gnu/packages/patches/bowtie-fix-makefile.patch b/gnu/packages/patches/bowtie-fix-makefile.patch
deleted file mode 100644
index 5ac65731cb..0000000000
--- a/gnu/packages/patches/bowtie-fix-makefile.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-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