This is an automated email from the git hooks/post-receive script.
guix_mirror_bot pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new f18a45499a gnu: bowtie: Update to 2.5.4.
f18a45499a is described below
commit f18a45499a810fb29d7d06930e4c41ba77730259
Author: Cayetano Santos <[email protected]>
AuthorDate: Fri Jan 9 13:28:50 2026 +0100
gnu: bowtie: Update to 2.5.4.
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.5.4.
[source]: Use G-Expressions in ’snippet.
[arguments]: Use G-Expressions.
<#:make-flags>: Add CC.
<#:phases>: Add ’tests? arguments to ’check phase; add ’fix-prefix.
[inputs]: Drop variables, add onetbb, delete tbb-2020 and
python-wrapper.
[native-inputs]: Add python-wrapper, which and perl-file-which.
Merges guix/guix!5491
Change-Id: I12686b06911c11170748b64af722c5311b2e542d
---
gnu/packages/bioinformatics.scm | 72 ++++++++++++++++++++++++-----------------
1 file changed, 42 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dc99eb5132..c9c8c87c02 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -138,6 +138,7 @@
#:use-module (gnu packages node)
#:use-module (gnu packages nss)
#:use-module (gnu packages ocaml)
+ #:use-module (gnu packages oneapi)
#:use-module (gnu packages pcre)
#:use-module (gnu packages package-management)
#:use-module (gnu packages parallel)
@@ -5674,7 +5675,7 @@ errors at the end of reads.")
(define-public bowtie
(package
(name "bowtie")
- (version "2.3.4.3")
+ (version "2.5.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -5683,40 +5684,51 @@ errors at the end of reads.")
(file-name (git-file-name name version))
(sha256
(base32
- "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp"))
- (modules '((guix build utils)))
+ "020dwg059zmgqcfnxgg67qmn8rf207mwrybly39ncch1riva58z5"))
(snippet
- '(begin
- (substitute* "Makefile"
- ;; replace BUILD_HOST and BUILD_TIME for deterministic
build
- (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
- (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))))
+ #~(begin
+ (use-modules (guix build utils))
+ (substitute* "Makefile"
+ ;; replace BUILD_HOST and BUILD_TIME for deterministic
build
+ (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))))
(build-system gnu-build-system)
(arguments
- `(#:make-flags
- ,#~(list "allall"
- "WITH_TBB=1"
- (string-append "prefix=" #$output))
- #:phases
- (modify-phases %standard-phases
- (replace 'configure
- (lambda _
- ;; This "extended character" is not considered valid.
- (substitute* "processor_support.h"
- (("“") "\"")
- (("”") "\""))))
- (replace 'check
- (lambda _
- (invoke "perl"
- "scripts/test/simple_tests.pl"
- "--bowtie2=./bowtie2"
- "--bowtie2-build=./bowtie2-build"))))))
+ (list
+ #:make-flags
+ #~(list "allall"
+ "WITH_TBB=1"
+ (string-append "prefix=" #$output)
+ (string-append "CC=" #$(cc-for-target)))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-prefix
+ (lambda _
+ (substitute* "Makefile"
+ (("/usr/local") #$output))))
+ (replace 'configure
+ (lambda _
+ ;; This "extended character" is not considered valid.
+ (substitute* "processor_support.h"
+ (("“") "\"")
+ (("”") "\""))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "perl"
+ "scripts/test/simple_tests.pl"
+ "--bowtie2=./bowtie2"
+ "--bowtie2-build=./bowtie2-build")))))))
(inputs
- `(("tbb" ,tbb-2020)
- ("zlib" ,zlib)
- ("python" ,python-wrapper)))
+ (list onetbb zlib))
(native-inputs
- (list perl perl-clone perl-test-deep perl-test-simple))
+ (list perl
+ perl-clone
+ perl-file-which
+ perl-test-deep
+ perl-test-simple
+ python-wrapper
+ which))
(home-page "https://bowtie-bio.sourceforge.net/bowtie2/index.shtml";)
(synopsis "Fast and sensitive nucleotide sequence read aligner")
(description
