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gnu: freebayes: Update to 1.3.9.

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* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.9.
[inputs]: Add bzip2 and xz.
[native-inputs]: Drop labels; remove bash-tap and test-simple-bash-src; add
perl6-tap-harness.
[arguments]: Remove phase 'unpack-submodule-sources; adjust other phases.

Change-Id: I7448a95882ae3a900e697f23824abe40444d039c
This commit is contained in:
Ricardo Wurmus 2025-04-03 17:07:06 +02:00
parent e0c92dd647
commit efaa20d2d8
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GPG key ID: 197A5888235FACAC
1 changed files with 45 additions and 58 deletions
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gnu/packages/bioinformatics.scm
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@ -141,6 +141,7 @@
#:use-module (gnu packages perl) #:use-module (gnu packages perl)
#:use-module (gnu packages perl-check) #:use-module (gnu packages perl-check)
#:use-module (gnu packages perl-web) #:use-module (gnu packages perl-web)
#:use-module (gnu packages perl6)
#:use-module (gnu packages pkg-config) #:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt) #:use-module (gnu packages popt)
#:use-module (gnu packages protobuf) #:use-module (gnu packages protobuf)
@ -22503,68 +22504,54 @@ manipulations on VCF files.")
(define-public freebayes (define-public freebayes
(package (package
(name "freebayes") (name "freebayes")
(version "1.3.7") (version "1.3.9")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/freebayes/freebayes") (url "https://github.com/freebayes/freebayes")
(commit (string-append "v" version)))) (commit (string-append "v" version))
(recursive? #true)))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 "163nd1xkq547za80khlys4qkgal64f3sgl6ap3yvik68r0rgyisv")))) (base32 "18i8xv5cx4n9924f4gqjk2sg3vi437nh7ssy99ng8ajschgaw1m2"))))
(build-system meson-build-system) (build-system meson-build-system)
(inputs (inputs
(list fastahack htslib smithwaterman tabixpp vcflib)) (list bzip2 fastahack htslib smithwaterman tabixpp vcflib xz))
(native-inputs (native-inputs
`(("bash-tap" ,bash-tap) (list bc
("bc" ,bc) grep ; Built with perl support.
("grep" ,grep) ; Built with perl support. parallel
("parallel" ,parallel) perl
("perl" ,perl) perl6-tap-harness
("pkg-config" ,pkg-config) pkg-config
("python" ,python) python
("samtools" ,samtools) samtools
("simde" ,simde) simde))
;; This submodule is needed to run the tests.
("test-simple-bash-src"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ingydotnet/test-simple-bash/")
(commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
(file-name "test-simple-bash-src-checkout")
(sha256
(base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:phases
`(modify-phases %standard-phases
(add-after 'unpack 'patch-source (add-after 'unpack 'patch-source
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(let ((bash-tap (assoc-ref inputs "bash-tap"))) (setenv "CPLUS_INCLUDE_PATH"
(substitute* (find-files "test/t") (string-append (getcwd) "/contrib/multichoose:"
(("BASH_TAP_ROOT=bash-tap") (getenv "CPLUS_INCLUDE_PATH")))
(string-append "BASH_TAP_ROOT=" bash-tap "/bin"))
(("bash-tap/bash-tap-bootstrap")
(string-append bash-tap "/bin/bash-tap-bootstrap"))
(("source.*bash-tap-bootstrap")
(string-append "source " bash-tap "/bin/bash-tap-bootstrap")))
(substitute* '("src/BedReader.cpp" (substitute* '("src/BedReader.cpp"
"src/BedReader.h") "src/BedReader.h")
(("../intervaltree/IntervalTree.h") "IntervalTree.h")) (("intervaltree/IntervalTree.h") "vcflib/IntervalTree.h")
;; We don't have Perl support in grep -E. (("<IntervalTree.h>") "<vcflib/IntervalTree.h>"))
(substitute* '("test/t/01_call_variants.t" (substitute* '("src/AlleleParser.h"
"test/t/01b_call_variants.t") "src/ResultData.h")
(("grep -P") "grep -E") (("Variant.h") "vcflib/Variant.h"))
(("\\\\t") " ")) (substitute* (find-files "." "\\.(h|c)(pp)?$")
(("\"multichoose.h\"") "<vcflib/multichoose.h>")
(("\"convert.h\"") "<smithwaterman/convert.h>")
(("\"split.h\"") "<fastahack/split.h>")
(("\"join.h\"") "<vcflib/join.h>"))
(substitute* "meson.build" (substitute* "meson.build"
;; Our pkg-config file is vcflib.pc ;; Our pkg-config file is vcflib.pc
(("libvcflib") "vcflib") (("libvcflib") "vcflib")
(("vcflib_inc,") ""))))) (("vcflib_inc,") ""))))
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "test/test-simple-bash")
(copy-recursively (assoc-ref inputs "test-simple-bash-src")
"test/test-simple-bash")))
;; The slow tests take longer than the specified timeout. ;; The slow tests take longer than the specified timeout.
,@(if (any (cute string=? <> (%current-system)) ,@(if (any (cute string=? <> (%current-system))
'("armhf-linux" "aarch64-linux")) '("armhf-linux" "aarch64-linux"))