Subject: bug#28802: closed (Re: [PATCH] gnu: Add paml.)

From: [email-masked] (GNU bug Tracking System)
Date: Fri, 13 Oct 2017 09:17:03 +0000

Your bug report

#28802: [PATCH] gnu: Add paml.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
28802: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=28802
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: Re: [PATCH] gnu: Add paml.
From: Ricardo Wurmus <[email-masked]>
To: [email-masked]
Date: Fri, 13 Oct 2017 11:15:56 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

> +                   (docs    '("Bismark_User_Guide.pdf"
> +                              "RELEASE_NOTES.txt")))

I removed this, because it is not used.
“guix lint” does not complain, so I pushed it to master.

-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Subject: [PATCH] gnu: Add paml.
From: Ricardo Wurmus <[email-masked]>
To: [email-masked]
Cc: Ricardo Wurmus <[email-masked]>
Date: Thu, 12 Oct 2017 23:56:32 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

From: Ricardo Wurmus <[email-masked]>

* gnu/packages/bioinformatics.scm (paml): New variable.
---
 gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9a47b076c..2de57d447 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10085,3 +10085,53 @@ straight away.  Its main features are:
   and CHH context
 @end itemize\n")
     (license license:gpl3+)))
+
+(define-public paml
+  (package
+    (name "paml")
+    (version "4.9e")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://abacus.gene.ucl.ac.uk/software/"
+                                  "paml" version ".tgz"))
+              (sha256
+               (base32
+                "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6"))
+              (modules '((guix build utils)))
+              ;; Remove Windows binaries
+              (snippet
+               '(begin
+                  (for-each delete-file (find-files "." "\\.exe$"))
+                  #t))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are no tests
+       #:make-flags '("CC=gcc")
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda _
+             (substitute* "src/BFdriver.c"
+               (("/bin/bash") (which "bash")))
+             (chdir "src")
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((tools '("baseml" "basemlg" "codeml"
+                            "pamp" "evolver" "yn00" "chi2"))
+                   (bin    (string-append (assoc-ref outputs "out") "/bin"))
+                   (docdir (string-append (assoc-ref outputs "out")
+                                           "/share/doc/paml"))
+                   (docs    '("Bismark_User_Guide.pdf"
+                              "RELEASE_NOTES.txt")))
+               (mkdir-p bin)
+               (for-each (lambda (file) (install-file file bin)) tools)
+               (copy-recursively "../doc" docdir)
+               #t))))))
+    (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html")
+    (synopsis "Phylogentic analysis by maximum likelihood")
+    (description "PAML (for Phylogentic Analysis by Maximum Likelihood)
+contains a few programs for model fitting and phylogenetic tree reconstruction
+using nucleotide or amino-acid sequence data.")
+    ;; GPLv3 only
+    (license license:gpl3)))
-- 
2.14.1