gnu: bcftools: Update to 1.14.
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14. (bcftools-1.12): New variable. (bcftools-1.10): Use package/inherit and delete trailing #t. [name]: Delete field.
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@ -373,7 +373,7 @@ (define-public bamutils
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(define-public bcftools
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(define-public bcftools
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(package
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(package
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(name "bcftools")
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(name "bcftools")
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(version "1.12")
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(version "1.14")
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(source (origin
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(source (origin
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(method url-fetch)
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(method url-fetch)
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(uri (string-append "https://github.com/samtools/bcftools/"
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(uri (string-append "https://github.com/samtools/bcftools/"
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@ -381,12 +381,11 @@ (define-public bcftools
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version "/bcftools-" version ".tar.bz2"))
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version "/bcftools-" version ".tar.bz2"))
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(sha256
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(sha256
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(base32
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(base32
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"1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks"))
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"1jqrma16fx8kpvb3c0462dg0asvmiv5yi8myqmc5ddgwi6p8ivxp"))
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(modules '((guix build utils)))
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(modules '((guix build utils)))
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(snippet '(begin
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(snippet '(begin
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;; Delete bundled htslib.
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;; Delete bundled htslib.
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(delete-file-recursively "htslib-1.12")
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(delete-file-recursively "htslib-1.14")))))
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#t))))
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(arguments
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(arguments
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`(#:configure-flags
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`(#:configure-flags
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@ -397,8 +396,7 @@ (define-public bcftools
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(add-before 'check 'patch-tests
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(add-before 'check 'patch-tests
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(lambda _
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(lambda _
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(substitute* "test/test.pl"
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(substitute* "test/test.pl"
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(("/bin/bash") (which "bash")))
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(("/bin/bash") (which "bash"))))))))
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#t)))))
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(native-inputs
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(native-inputs
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(list htslib perl))
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(list htslib perl))
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(inputs
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(inputs
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@ -412,9 +410,25 @@ (define-public bcftools
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;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
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;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
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(license (list license:gpl3+ license:expat))))
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(license (list license:gpl3+ license:expat))))
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(define-public bcftools-1.12
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(package/inherit bcftools
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(version "1.12")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/samtools/bcftools/"
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"releases/download/"
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version "/bcftools-" version ".tar.bz2"))
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(sha256
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(base32
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"1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks"))
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(modules '((guix build utils)))
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(snippet '(begin
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;; Delete bundled htslib.
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(delete-file-recursively "htslib-1.12")))))
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(native-inputs (list htslib-1.12 perl))))
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(define-public bcftools-1.10
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(define-public bcftools-1.10
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(package (inherit bcftools)
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(package/inherit bcftools
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(name "bcftools")
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(version "1.10")
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(version "1.10")
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(source (origin
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(source (origin
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(method url-fetch)
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(method url-fetch)
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@ -427,11 +441,8 @@ (define-public bcftools-1.10
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(modules '((guix build utils)))
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(modules '((guix build utils)))
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(snippet '(begin
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(snippet '(begin
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;; Delete bundled htslib.
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;; Delete bundled htslib.
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(delete-file-recursively "htslib-1.10")
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(delete-file-recursively "htslib-1.10")))))
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#t))))
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(native-inputs (list htslib-1.10 perl))))
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(build-system gnu-build-system)
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(native-inputs
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(list htslib-1.10 perl))))
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(define-public bedops
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(define-public bedops
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(package
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(package
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