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gnu: proteinortho: Update to 6.0.14.

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* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14.
[source]: Fetch from git; remove pre-built scripts.
[arguments]: Set make-flags; update wrap-programs phase to wrap all scripts.
[inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove
python-2.
[native-inputs]: Add which.
[license]: Update to GPLv3+
This commit is contained in:
Ricardo Wurmus 2020-02-26 14:05:36 +01:00
parent 9207575669
commit 146430ea0e
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GPG key ID: 197A5888235FACAC
1 changed files with 33 additions and 19 deletions
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@ -4921,20 +4921,26 @@ predicts the locations of structural units in the sequences.")
(define-public proteinortho (define-public proteinortho
(package (package
(name "proteinortho") (name "proteinortho")
(version "5.16b") (version "6.0.14")
(source (source (origin
(origin (method git-fetch)
(method url-fetch) (uri (git-reference
(uri (url "https://gitlab.com/paulklemm_PHD/proteinortho.git")
(string-append (commit (string-append "v" version))))
"http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" (file-name (git-file-name name version))
version "_src.tar.gz"))
(sha256 (sha256
(base32 (base32
"1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j")))) "0pmy617zy2z2w6hjqxjhf3rzikf5n3mpia80ysq8233vfr7wrzff"))
(modules '((guix build utils)))
(snippet
'(begin
;; remove pre-built scripts
(delete-file-recursively "src/BUILD/")
#t))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:test-target "test" `(#:test-target "test"
#:make-flags '("CC=gcc")
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(replace 'configure (replace 'configure
@ -4952,15 +4958,23 @@ predicts the locations of structural units in the sequences.")
#t)) #t))
(add-after 'install 'wrap-programs (add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((path (getenv "PATH")) (let ((path (getenv "PATH"))
(out (assoc-ref outputs "out")) (out (assoc-ref outputs "out")))
(binary (string-append out "/bin/proteinortho5.pl"))) (for-each (lambda (script)
(wrap-program binary `("PATH" ":" prefix (,path)))) (wrap-script script `("PATH" ":" prefix (,path))))
(cons (string-append out "/bin/proteinortho")
(find-files out "\\.(pl|py)$"))))
#t))))) #t)))))
(inputs (inputs
`(("perl" ,perl) `(("guile" ,guile-3.0) ; for wrap-script
("python" ,python-2) ("diamond" ,diamond)
("blast+" ,blast+))) ("perl" ,perl)
("python" ,python-wrapper)
("blast+" ,blast+)
("lapack" ,lapack)
("openblas" ,openblas)))
(native-inputs
`(("which" ,which)))
(home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
(synopsis "Detect orthologous genes across species") (synopsis "Detect orthologous genes across species")
(description (description
@ -4968,7 +4982,7 @@ predicts the locations of structural units in the sequences.")
species. For doing so, it compares similarities of given gene sequences and species. For doing so, it compares similarities of given gene sequences and
clusters them to find significant groups. The algorithm was designed to handle clusters them to find significant groups. The algorithm was designed to handle
large-scale data and can be applied to hundreds of species at once.") large-scale data and can be applied to hundreds of species at once.")
(license license:gpl2+))) (license license:gpl3+)))
(define-public pyicoteo (define-public pyicoteo
(package (package