Re: Update mafft to 7.245.

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

[-- Attachment #1: Type: text/plain, Size: 1399 bytes --]

Two reviews in record time, nice.

On 10/11/15 23:12, Efraim Flashner wrote:
> On Tue, 10 Nov 2015 22:18:10 +1000
> Ben Woodcroft <b.woodcroft@uq.edu.au> wrote:
>
>> Also had to fix the inputs. Hard not to notice these things in the
>> environment container - worked well thanks.
> Do they need to be propagated inputs? Did you try them as native-inputs?
> Often that's enough to take care of it.
The main program 'mafft' is actually a reasonably long shell script, 
which itself calls awk, grep, perl, etc. collectively many times (>100 I 
would guess). I think it is intended to be run where these programs are 
available. I could do as Ricardo suggests and run substitute* but this 
seems a bit error-prone and not very future-proof to me, especially when 
the shell script is difficult to exhaustively test. WDYT?

Note that mafft is probably not going to remain as a leaf because a 
number of bioinformatic tools not yet packaged rely on it.
> Also, instead of:
> Fix inputs.
> the commit message is more along the lines of:
>    [inputs]: Move inputs to propagated-inputs and add missing dependencies.
> but I normally have to check against older commit messages to see what others
> are doing and I try to copy that.
Hopefully the attached is a better attempt? I also added another small 
improvement, not distributing the manpage of a program that is excluded 
from distribution.

Thanks.



[-- Attachment #2: 0001-gnu-mafft-Update-to-7.245.patch --]
[-- Type: text/x-patch, Size: 2705 bytes --]

From e05c50d2b40bf3290ec247223b3504429e9ad44e Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 11 Nov 2015 08:04:55 +1000
Subject: [PATCH] gnu: mafft: Update to 7.245.

* gnu/packages/bioinformatics.scm (mafft): Update to 7.245.
[arguments]: Don't include mafft-homologs manpage.
[inputs]: Move inputs to propagated-inputs and add missing dependencies.
---
 gnu/packages/bioinformatics.scm | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f13e405..9ee669e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -40,6 +40,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpio)
   #:use-module (gnu packages file)
+  #:use-module (gnu packages gawk)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages machine-learning)
@@ -1688,7 +1689,7 @@ sequencing tag position and orientation.")
 (define-public mafft
   (package
     (name "mafft")
-    (version "7.221")
+    (version "7.245")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1697,7 +1698,7 @@ sequencing tag position and orientation.")
               (file-name (string-append name "-" version ".tgz"))
               (sha256
                (base32
-                "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d"))))
+                "0m1l7gdrmfxjw54d3a0g18w6rwqrra9w9zvxix7dcddw6d1qyir2"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no automated tests, though there are tests in the read me
@@ -1718,6 +1719,9 @@ sequencing tag position and orientation.")
               ;; remove mafft-homologs.rb from SCRIPTS
               (("^SCRIPTS = mafft mafft-homologs.rb")
                "SCRIPTS = mafft")
+              ;; remove mafft-homologs from MANPAGES
+              (("^MANPAGES = mafft.1 mafft-homologs.1")
+               "MANPAGES = mafft.1")
               ;; remove mafft-distance from PROGS
               (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
                "PROGS = dvtditr dndfast7 dndblast sextet5")
@@ -1731,8 +1735,11 @@ sequencing tag position and orientation.")
 \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
             #t))
          (delete 'configure))))
-    (inputs
-     `(("perl" ,perl)))
+    (propagated-inputs
+     `(("perl" ,perl)
+       ("gawk" ,gawk)
+       ("coreutils" ,coreutils)
+       ("grep" ,grep)))
     (home-page "http://mafft.cbrc.jp/alignment/software/")
     (synopsis "Multiple sequence alignment program")
     (description
-- 
2.4.3