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.
This commit is contained in:
Ricardo Wurmus
parent
2d12284d38
commit
0047d26a22
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@ -416,7 +416,6 @@ dist_patch_DATA = \
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gnu/packages/patches/avidemux-install-to-lib.patch \
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gnu/packages/patches/avrdude-fix-libusb.patch \
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gnu/packages/patches/bash-completion-directories.patch \
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gnu/packages/patches/bowtie-fix-makefile.patch \
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gnu/packages/patches/bigloo-gc-shebangs.patch \
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gnu/packages/patches/binutils-ld-new-dtags.patch \
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gnu/packages/patches/binutils-loongson-workaround.patch \
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@ -1,5 +1,5 @@
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
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;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
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@ -603,7 +603,7 @@ errors at the end of reads.")
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(define-public bowtie
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(package
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(name "bowtie")
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(version "2.2.4")
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(version "2.2.6")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
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@ -611,42 +611,36 @@ errors at the end of reads.")
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
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"1ssfvymxfrap6f9pf86s9bvsbqdgka4abr2r7j3mgr4w1l289m86"))
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(modules '((guix build utils)))
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(snippet
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'(substitute* "Makefile"
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(("^CC = .*$") "CC = gcc")
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(("^CPP = .*$") "CPP = g++")
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;; replace BUILD_HOST and BUILD_TIME for deterministic build
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(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
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(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
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(patches (list (search-patch "bowtie-fix-makefile.patch")))))
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(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
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(build-system gnu-build-system)
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(inputs `(("perl" ,perl)
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("perl-clone" ,perl-clone)
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("perl-test-deep" ,perl-test-deep)
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("perl-test-simple" ,perl-test-simple)
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("python" ,python-2)))
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("python" ,python-2)
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("tbb" ,tbb)))
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(arguments
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'(#:make-flags '("allall")
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'(#:make-flags
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(list "allall"
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"WITH_TBB=1"
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(string-append "prefix=" (assoc-ref %outputs "out")))
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#:phases
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(alist-delete
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'configure
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(alist-replace
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'install
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'check
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
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(for-each (lambda (file)
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(install-file file bin))
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(find-files "." "bowtie2.*"))))
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(alist-replace
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'check
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(lambda* (#:key outputs #:allow-other-keys)
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(system* "perl"
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"scripts/test/simple_tests.pl"
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"--bowtie2=./bowtie2"
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"--bowtie2-build=./bowtie2-build"))
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%standard-phases)))))
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(system* "perl"
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"scripts/test/simple_tests.pl"
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"--bowtie2=./bowtie2"
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"--bowtie2-build=./bowtie2-build"))
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%standard-phases))))
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(home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
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(synopsis "Fast and sensitive nucleotide sequence read aligner")
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(description
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@ -1,31 +0,0 @@
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From 4a99b0023bdfbbe486b9649489a32ea184c18c9a Mon Sep 17 00:00:00 2001
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From: Valentin Antonescu <valentin@jhu.edu>
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Date: Tue, 2 Dec 2014 11:19:13 -0500
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Subject: [PATCH] Make sure the Mavericks test happens only under Darwin.
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---
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Makefile | 11 +++++------
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1 file changed, 5 insertions(+), 6 deletions(-)
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diff --git a/Makefile b/Makefile
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index d74f7c8..a4cdfa7 100644
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--- a/Makefile
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+++ b/Makefile
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@@ -54,12 +54,11 @@ endif
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MACOS = 0
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ifneq (,$(findstring Darwin,$(shell uname)))
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MACOS = 1
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-endif
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-
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-ifneq (,$(findstring 13,$(shell uname -r)))
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- CPP = clang++
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- CC = clang
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- EXTRA_FLAGS += -stdlib=libstdc++
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+ ifneq (,$(findstring 13,$(shell uname -r)))
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+ CPP = clang++
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+ CC = clang
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+ EXTRA_FLAGS += -stdlib=libstdc++
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+ endif
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endif
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POPCNT_CAPABILITY ?= 1
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