From mboxrd@z Thu Jan  1 00:00:00 1970
From: Ricardo Wurmus <rekado@elephly.net>
Subject: Re: [PATCH] Add MAFFT.
Date: Sat, 25 Jul 2015 21:26:50 +0200
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To: Ben Woodcroft <b.woodcroft@uq.edu.au>
Cc: "guix-devel@gnu.org" <guix-devel@gnu.org>

Hi Ben,

> +       #:phases
> +       (modify-phases %standard-phases
> +         (add-after 'unpack 'enter-dir
> +                    (lambda _ (chdir "core") #t))
> +         ;; on advice from the MAFFT authors, do not distribute mafft-profile,
> +         ;; mafft-distance mafft-homologs.rb

What does this mean?  Are they non-free software?  If so, they should be
removed in a snippet.

> +         (add-after 'enter-dir 'patch-makefile
> +                    (lambda _
> +                      (substitute* "Makefile"
> +                        (("^SCRIPTS = mafft mafft-homologs.rb")
> +                         "SCRIPTS = mafft")
> +                        (((string-append "^PROGS = dvtditr dndfast7 dndblast"
> +                                         " sextet5 mafft-distance"))
> +                         "PROGS = dvtditr dndfast7 dndblast sextet5")
> +                        (((string-append "splittbfast disttbfast tbfast "
> +                                         "mafft-profile f2cl mccaskillwrap"))
> +                         "splittbfast disttbfast tbfast f2cl mccaskillwrap")

This line looks particularly unclear.  It took me a little too long to
find the difference in the replacement.  Is there a nicer regular
expression that you could use to indicate the removal of
“mafft-profile”?

> +                        (("^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 for unix-like operating systems")

Please remove “for unix-like operating systems”.

> +    (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."))))

~~ Ricardo