gnu: gemma: Refresh package style.

* 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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@ -8691,52 +8691,48 @@ comment or quality sections.")
(define-public gemma
(package
(name "gemma")
(version "v0.98.5")
(version "0.98.5")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/genetics-statistics/GEMMA")
(commit version)))
(url "https://github.com/genetics-statistics/GEMMA")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1dm8pf1fbdmv2yiz5aybcvk3050m5350gq8xlr4j6swzm3wwhydn"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file-recursively "contrib")
#t))))
#~(begin
(delete-file-recursively "contrib")))))
(build-system gnu-build-system)
(inputs
(list gsl openblas zlib))
(native-inputs
`(("catch" ,catch2-1)
("perl" ,perl)
("shunit2" ,shunit2)
("which" ,which)))
(list catch2-1
perl
shunit2
which))
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'prepare-build
(lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "bin")
(substitute* "Makefile"
(("/usr/local/opt/openblas")
(assoc-ref inputs "openblas")))
#t))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; 'make slow-check' expects shunit2-2.0.3.
(with-directory-excursion "test"
(invoke "./test_suite.sh"))
#t)))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(install-file "bin/gemma"
(string-append (assoc-ref outputs "out") "/bin"))
#t)))))
(list
#:phases
#~(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'prepare-build
(lambda _
(mkdir-p "bin")
(substitute* "Makefile"
(("/usr/local/opt/openblas")
#$(this-package-input "openblas")))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; 'make slow-check' expects shunit2-2.0.3.
(with-directory-excursion "test"
(invoke "./test_suite.sh")))))
(replace 'install
(lambda _
(install-file "bin/gemma" (string-append #$output "/bin")))))))
(home-page "https://github.com/genetics-statistics/GEMMA")
(synopsis "Tool for genome-wide efficient mixed model association")
(description