03/03: gnu: proteinortho: Update to 6.0.14.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 146430ea0e0008ff91972f944920dfa01d1ab360
Author: Ricardo Wurmus <address@hidden>
AuthorDate: Wed Feb 26 14:05:36 2020 +0100

    gnu: proteinortho: Update to 6.0.14.
    
    * 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+
---
 gnu/packages/bioinformatics.scm | 52 ++++++++++++++++++++++++++---------------
 1 file changed, 33 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 546be38..8ed13b2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4921,20 +4921,26 @@ predicts the locations of structural units in the 
sequences.")
 (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
@@ -4952,15 +4958,23 @@ predicts the locations of structural units in the 
sequences.")
              #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
@@ -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
 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