Re: Update mafft to 7.245.

[Ben Woodcroft]

On 11/12/15 02:16, Ricardo Wurmus wrote:
> Ben Woodcroft <address@hidden> writes:
>
> > 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 <address@hidden> 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?
> I looked at the instances of “perl”, “awk”, and “grep” and they seem
> manageable.  I didn’t test this but attached is a different version of
> your patch that does what I suggested.  It might work.  Could you try to
> confirm that it’s okay?
>
> What do you think?
I think you are quite valiant. As I say, I cannot be confident in my 
testing (even those in the readme). The diff looked mostly fine by eye, 
but there was some issues near the end which mangled things somewhat 
(although maybe not the result, not sure). How's the attached? I upped 
version too. OK?

Thanks,
ben

0001-PATCH-gnu-mafft-Update-to-7.267.patch
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