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(-)

(limited to 'gnu/packages')

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 @@ 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
-- 
cgit v1.2.3