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gnu: bowtie: Update to 2.5.4.

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* 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.

Change-Id: I12686b06911c11170748b64af722c5311b2e542d
This commit is contained in:
Cayetano Santos 2026-01-09 13:28:50 +01:00
parent b155bcbe4d
commit a3876851f7
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GPG key ID: BF5CDF4DF6BF6682
1 changed files with 42 additions and 30 deletions
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72
gnu/packages/bioinformatics.scm
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@ -137,6 +137,7 @@
#: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)
@ -5673,7 +5674,7 @@ 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
@ -5682,40 +5683,51 @@ 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