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gnu: proteinortho: Update to 6.3.2.

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* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.3.2.
[source]: Adjust snippet to also delete lapack source tarball.
[arguments]: Rewrite using g-expressions.  Add flag to run tests
sequentially.  Adjust make-flags for cross-compiling and to set PREFIX.
Delete 'configure and custom 'configure phase.  Remove trailing #t from
phases.

Change-Id: I40249e5ac92c26223119b81b4677c08d5ab230e6
This commit is contained in:
Efraim Flashner 2024-05-06 22:49:35 +03:00
parent d967ffb367
commit dd23efe020
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GPG Key ID: 41AAE7DCCA3D8351
1 changed files with 28 additions and 33 deletions
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@ -8984,7 +8984,7 @@ predicts the locations of structural units in the sequences.")
(define-public proteinortho (define-public proteinortho
(package (package
(name "proteinortho") (name "proteinortho")
(version "6.0.14") (version "6.3.2")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -8993,45 +8993,40 @@ predicts the locations of structural units in the sequences.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0pmy617zy2z2w6hjqxjhf3rzikf5n3mpia80ysq8233vfr7wrzff")) "0p8iaxq193fh67hw3cydvdah1vz1c3f18227gj1mhkww0ms7g6xa"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(begin
;; remove pre-built scripts ;; Remove pre-built scripts and source tarballs.
(delete-file-recursively "src/BUILD/") (delete-file-recursively "src/BUILD/")
#t)))) (delete-file "src/lapack-3.8.0.tar.gz")))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:test-target "test" (list
#:make-flags '("CC=gcc") #:test-target "test"
#:parallel-tests? #f
#:make-flags
#~(list (string-append "CC=" #$(cc-for-target))
(string-append "CXX=" #$(cxx-for-target))
(string-append "PREFIX=" #$output)
(string-append "INSTALLDIR=" #$output "/bin"))
#:phases #:phases
(modify-phases %standard-phases #~(modify-phases %standard-phases
(replace 'configure (delete 'configure)
;; There is no configure script, so we modify the Makefile directly. (add-before 'install 'make-install-directory
(lambda* (#:key outputs #:allow-other-keys) ;; The install directory is not created during 'make install'.
(substitute* "Makefile" (lambda* (#:key outputs #:allow-other-keys)
(("INSTALLDIR=.*") (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))))
(string-append (add-after 'install 'wrap-programs
"INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")) (lambda* (#:key inputs outputs #:allow-other-keys)
(("-llapack -lblas") (let ((path (getenv "PATH"))
"-lopenblas")) (out (assoc-ref outputs "out"))
#t)) (guile (search-input-file inputs "bin/guile")))
(add-before 'install 'make-install-directory (for-each (lambda (script)
;; The install directory is not created during 'make install'. (wrap-script script #:guile guile
(lambda* (#:key outputs #:allow-other-keys) `("PATH" ":" prefix (,path))))
(mkdir-p (string-append (assoc-ref outputs "out") "/bin")) (cons (string-append out "/bin/proteinortho")
#t)) (find-files out "\\.(pl|py)$")))))))))
(add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((path (getenv "PATH"))
(out (assoc-ref outputs "out"))
(guile (search-input-file inputs "bin/guile")))
(for-each (lambda (script)
(wrap-script script #:guile guile
`("PATH" ":" prefix (,path))))
(cons (string-append out "/bin/proteinortho")
(find-files out "\\.(pl|py)$"))))
#t)))))
(inputs (inputs
`(("guile" ,guile-3.0) ; for wrap-script `(("guile" ,guile-3.0) ; for wrap-script
("diamond" ,diamond) ("diamond" ,diamond)