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gnu: gemma: Refresh package style.

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* gnu/packages/bioinformatics.scm (gemma): Apply G-Expressions, remove
trailing #t from procedures and lambdas, fix indentation.
[version]: Remove "v" to improve format, seen in
<https://codeberg.org/guix/guix/pulls/3009#issuecomment-7390966>.
[source] <uri>: Add "v" to {commit} field.
[native-inputs]: Remove labels.

Change-Id: I9c2113dbdc265e3726b548670d450d0cdcbf1bea
This commit is contained in:
Sharlatan Hellseher 2025-09-26 12:54:19 +01:00
parent 593cd7f73f
commit 56e892e100
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GPG key ID: 76D727BFF62CD2B5
1 changed files with 28 additions and 32 deletions
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gnu/packages/bioinformatics.scm
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@ -8691,52 +8691,48 @@ comment or quality sections.")
(define-public gemma (define-public gemma
(package (package
(name "gemma") (name "gemma")
(version "v0.98.5") (version "0.98.5")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/genetics-statistics/GEMMA") (url "https://github.com/genetics-statistics/GEMMA")
(commit version))) (commit (string-append "v" version))))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1dm8pf1fbdmv2yiz5aybcvk3050m5350gq8xlr4j6swzm3wwhydn")) "1dm8pf1fbdmv2yiz5aybcvk3050m5350gq8xlr4j6swzm3wwhydn"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin #~(begin
(delete-file-recursively "contrib") (delete-file-recursively "contrib")))))
#t))))
(build-system gnu-build-system) (build-system gnu-build-system)
(inputs (inputs
(list gsl openblas zlib)) (list gsl openblas zlib))
(native-inputs (native-inputs
`(("catch" ,catch2-1) (list catch2-1
("perl" ,perl) perl
("shunit2" ,shunit2) shunit2
("which" ,which))) which))
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:phases
(delete 'configure) #~(modify-phases %standard-phases
(add-after 'unpack 'prepare-build (delete 'configure)
(lambda* (#:key inputs #:allow-other-keys) (add-after 'unpack 'prepare-build
(mkdir-p "bin") (lambda _
(substitute* "Makefile" (mkdir-p "bin")
(("/usr/local/opt/openblas") (substitute* "Makefile"
(assoc-ref inputs "openblas"))) (("/usr/local/opt/openblas")
#t)) #$(this-package-input "openblas")))))
(replace 'check (replace 'check
(lambda* (#:key tests? #:allow-other-keys) (lambda* (#:key tests? #:allow-other-keys)
(when tests? (when tests?
;; 'make slow-check' expects shunit2-2.0.3. ;; 'make slow-check' expects shunit2-2.0.3.
(with-directory-excursion "test" (with-directory-excursion "test"
(invoke "./test_suite.sh")) (invoke "./test_suite.sh")))))
#t))) (replace 'install
(replace 'install (lambda _
(lambda* (#:key outputs #:allow-other-keys) (install-file "bin/gemma" (string-append #$output "/bin")))))))
(install-file "bin/gemma"
(string-append (assoc-ref outputs "out") "/bin"))
#t)))))
(home-page "https://github.com/genetics-statistics/GEMMA") (home-page "https://github.com/genetics-statistics/GEMMA")
(synopsis "Tool for genome-wide efficient mixed model association") (synopsis "Tool for genome-wide efficient mixed model association")
(description (description