diff options
| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-14 14:36:32 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-14 14:43:25 +0100 |
| commit | 0047d26a220805a99c84d9b87c73e012a63919e1 (patch) | |
| tree | 1428f2e8a83d00279caf7b0b9f90afb5442c45f7 /gnu/packages | |
| parent | 2d12284d389df5cbe05c7162397b929d9a4dbee6 (diff) | |
gnu: bowtie: Update to 2.2.6.
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 38 | ||||
| -rw-r--r-- | gnu/packages/patches/bowtie-fix-makefile.patch | 31 |
2 files changed, 16 insertions, 53 deletions
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 |