Ben Woodcroft <b.woodcroft@uq.edu.au> 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 <b.woodcroft@uq.edu.au> 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?