From 146430ea0e0008ff91972f944920dfa01d1ab360 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 26 Feb 2020 14:05:36 +0100
Subject: 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 546be38ab0..8ed13b22e5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4921,20 +4921,26 @@ (define-public prank
 (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 @@ (define-public proteinortho
              #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 @@ (define-public proteinortho
 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
-- 
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