Re: [PATCH] Add prodigal.

[Ben Woodcroft]

On 27/06/15 20:40, Ricardo Wurmus wrote:
> >   +    (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
> Shouldn’t “Archaea” and “Bacteria” both be lower-cased?
I don't believe so. As I understand it you can use "bacterial" and 
"archaeal" with lower case, but here we are referring to the domains as 
nouns.

I did take some small liberties here. The original sentence on the web was

>Fast, reliable protein-coding gene prediction for prokaryotic genomes.

To me this is problematic in two ways:
1. It works on more than just genomes
2. There is some contention in the field about the use of "prokaryote", 
since this refers to a paraphyletic group - us humans are more closely 
related to Archaea than Bacteria.
http://link.springer.com/referenceworkentry/10.1007/978-3-642-30194-0_114

I figure it was just easier to sidestep the issue and put Archaea and 
Bacteria.
> another thing just occurred to me.  Instead of replacing the install
> phase you might just overwrite the INSTALLDIR variable, something like
> this:
>
>      #:make-flags (list (string-append "INSTALLDIR="
>                                        (assoc-ref %outputs "out")))
>
> What do you think?
That made it more concise, and maybe more future proof (though need 
added "/bin").

0001-gnu-Add-prodigal.patch
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