On 07/09/15 18:55, Andreas Enge wrote:
On Tue, Aug 25, 2015 at 10:58:42PM +0200, Ludovic Courtès wrote:
It seems this message was left unanswered. Andreas?
I had a cursory look at the patch, here are some comments:
[..]
+protein sequences. For instance, it offers L-INS-i (accurate; for alignment
+of <???200 sequences) and FFT-NS-2 (fast; for alignment of <???30,000
Is this an artefact of the mailer?
I did not check whether the package passes "guix lint".
Could you send an updated patch?
Attached - I was only able to remove some of the long string-append
lines. Apologies for that second "patch" - not intentional. Thanks for
the review. I've changed the character to a different "~" so hopefully
more standard now. Guix lint doesn't complain.
ben
>From 0796e8be05977e6d30eab787a1550bd8d1f12b2d Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <[email protected]>
Date: Sat, 12 Sep 2015 22:10:20 +1000
Subject: [PATCH] gnu: Add mafft.
* gnu/packages/bioinformatics.scm (mafft): New variable.
---
gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 03eb2df..e0b7e40 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1543,6 +1543,66 @@ resolution of binding sites through combining the information of both
sequencing tag position and orientation.")
(license license:bsd-3)))
+(define-public mafft
+ (package
+ (name "mafft")
+ (version "7.221")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://mafft.cbrc.jp/alignment/software/mafft-"; version
+ "-without-extensions-src.tgz"))
+ (file-name (string-append name "-" version ".tgz"))
+ (sha256
+ (base32
+ "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no automated tests, though there are tests in the read me
+ #:make-flags (let ((out (assoc-ref %outputs "out")))
+ (list (string-append "PREFIX=" out)
+ (string-append "BINDIR="
+ (string-append out "/bin"))))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-dir
+ (lambda _ (chdir "core") #t))
+ (add-after 'enter-dir 'patch-makefile
+ (lambda _
+ ;; on advice from the MAFFT authors, there is no need to
+ ;; distribute mafft-profile, mafft-distance, or
+ ;; mafft-homologs.rb as they are too "specialised".
+ (substitute* "Makefile"
+ ;; remove mafft-homologs.rb from SCRIPTS
+ (("^SCRIPTS = mafft mafft-homologs.rb")
+ "SCRIPTS = mafft")
+ ;; remove mafft-distance from PROGS
+ (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
+ "PROGS = dvtditr dndfast7 dndblast sextet5")
+ ;; remove mafft-profile from PROGS
+ (((string-append "splittbfast disttbfast tbfast mafft-profile"
+ " f2cl mccaskillwrap"))
+ "splittbfast disttbfast tbfast f2cl mccaskillwrap")
+ (("^rm -f mafft-profile mafft-profile.exe") "#")
+ (("^rm -f mafft-distance mafft-distance.exe") ")#")
+ ;; do not install MAN pages in libexec folder
+ (((string-append "^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES"
+ "\\) \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)"))
+ "#"))
+ #t))
+ (delete 'configure))))
+ (inputs
+ `(("perl" ,perl)))
+ (home-page "http://mafft.cbrc.jp/alignment/software/";)
+ (synopsis
+ "Multiple sequence alignment program")
+ (description
+ "MAFFT offers a range of multiple alignment methods for nucleotide and
+protein sequences. For instance, it offers L-INS-i (accurate; for alignment
+of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
+sequences).")
+ (license (license:non-copyleft "file://license"
+ "See license in the distribution."))))
(define-public metabat
(package
--
2.4.3
