Re: [PATCH] Add MAFFT.

[ludo@gnu.org (Ludovic Courtès)]

Ben Woodcroft <b.woodcroft@uq.edu.au> skribis:

> From 0796e8be05977e6d30eab787a1550bd8d1f12b2d Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Sat, 12 Sep 2015 22:10:20 +1000
> Subject: [PATCH] gnu: Add mafft.
>
> * gnu/packages/bioinformatics.scm (mafft): New variable.

I’ll leave it to Ricardo, but two minor comments:

> +              (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\\)"))
> +                 "#"))

Maybe not a blocker, but I would really prefer to patterns to be literal
strings.  If they are too long, we can always split the literal over two
lines:

    "like \
this"

> +   (license (license:non-copyleft "file://license"
> +                                  "See license in the distribution."))))

I think this should be something like:

  (license (license:non-copyleft
             "http://mafft.cbrc.jp/alignment/software/license.txt"
             "BSD-3 with different formatting"))

Thanks,
Ludo’.