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gnu: freebayes: Update to 1.3.7.

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* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7.
[arguments]: Do not use "grep -P" in tests; drop trailing #T.
This commit is contained in:
Ricardo Wurmus 2023-04-27 11:40:09 +02:00
parent 133957f7bb
commit fa685c87ea
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GPG key ID: 197A5888235FACAC
1 changed files with 12 additions and 15 deletions
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gnu/packages/bioinformatics.scm
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@ -17339,7 +17339,7 @@ (define-public vcflib
(define-public freebayes
(package
(name "freebayes")
(version "1.3.5")
(version "1.3.7")
(source (origin
(method git-fetch)
(uri (git-reference
@ -17347,12 +17347,7 @@ (define-public freebayes
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file-recursively "contrib/htslib")
#t))))
(base32 "163nd1xkq547za80khlys4qkgal64f3sgl6ap3yvik68r0rgyisv"))))
(build-system meson-build-system)
(inputs
(list fastahack htslib smithwaterman tabixpp vcflib))
@ -17392,25 +17387,27 @@ (define-public freebayes
(substitute* '("src/BedReader.cpp"
"src/BedReader.h")
(("../intervaltree/IntervalTree.h") "IntervalTree.h"))
;; We don't have Perl support in grep -E.
(substitute* '("test/t/01_call_variants.t"
"test/t/01b_call_variants.t")
(("grep -P") "grep -E")
(("\\\\t") " "))
(substitute* "meson.build"
;; Our pkg-config file is vcflib.pc
(("libvcflib") "vcflib")
(("vcflib_inc,") ""))
#t)))
(("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")
#t))
"test/test-simple-bash")))
;; The slow tests take longer than the specified timeout.
,@(if (any (cute string=? <> (%current-system))
'("armhf-linux" "aarch64-linux"))
'((replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "meson" "test" "--timeout-multiplier" "5"))
#t)))
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "meson" "test" "--timeout-multiplier" "5")))))
'()))))
(home-page "https://github.com/freebayes/freebayes")
(synopsis "Haplotype-based variant detector")