(define-public proteinortho
(package
(name "proteinortho")
- (version "5.16b")
- (source
- (origin
- (method url-fetch)
- (uri
- (string-append
- "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
- version "_src.tar.gz"))
- (sha256
- (base32
- "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j"))))
+ (version "6.0.14")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/paulklemm_PHD/proteinortho.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0pmy617zy2z2w6hjqxjhf3rzikf5n3mpia80ysq8233vfr7wrzff"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; remove pre-built scripts
+ (delete-file-recursively "src/BUILD/")
+ #t))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
+ #:make-flags '("CC=gcc")
#:phases
(modify-phases %standard-phases
(replace 'configure
#t))
(add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((path (getenv "PATH"))
- (out (assoc-ref outputs "out"))
- (binary (string-append out "/bin/proteinortho5.pl")))
- (wrap-program binary `("PATH" ":" prefix (,path))))
+ (let ((path (getenv "PATH"))
+ (out (assoc-ref outputs "out")))
+ (for-each (lambda (script)
+ (wrap-script script `("PATH" ":" prefix (,path))))
+ (cons (string-append out "/bin/proteinortho")
+ (find-files out "\\.(pl|py)$"))))
#t)))))
(inputs
- `(("perl" ,perl)
- ("python" ,python-2)
- ("blast+" ,blast+)))
+ `(("guile" ,guile-3.0) ; for wrap-script
+ ("diamond" ,diamond)
+ ("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")
(synopsis "Detect orthologous genes across species")
(description
species. For doing so, it compares similarities of given gene sequences and
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.")
- (license license:gpl2+)))
+ (license license:gpl3+)))
(define-public pyicoteo
(package