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 <[email protected]> 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.
>From e05c50d2b40bf3290ec247223b3504429e9ad44e Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <[email protected]>
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
