Re: [PATCH] Add Ribotaper.

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

On 07/07/16 23:45, Ricardo Wurmus wrote:
> Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
>
>> On 07/07/16 19:26, Ricardo Wurmus wrote:
>>> Hi Guix,
>>>
>>> this patch adds a bioinformatics tool called "Ribotaper".  It needs a somewhat
>>> older version of bedtools, because the output format produced by bedtools
>>> changed after version 2.18.0 (they don't seem to care about semantic
>>> versioning).  This is why this patch not only adds a variable "ribotaper" but
>>> also "bedtools-for-ribotaper".
>>>
>>> Do you think I should rather name it "bedtools-2.18" and make it public so
>>> that users can install it?
>> This would be my preference, IIUC this is the current way we do this. Is
>> there any difference from previous times we've had to include outdated
>> packages?
> I actually prefer to just offer “bedtools-2.18” without restricting it
> to just ribotaper, but we’d have to ensure that this version stays
> around (adding a comment on top should be enough).
>
> We currently have “guile-for-guile-emacs”, which offers a variant of
> Guile, but the situation is slightly different here.  We also have
> “armadillo-for-rcpparmadillo”.  In both cases, the packages are not
> private.  In the former case the package name differs, but in the case
> of armadillo it’s only the variable name that indicates that this is
> special.
>
> I think in the ribotaper/bedtools case we should just name the variable
> “bedtools-2.18”  and make it public.

I agree with should call it 'bedtools-2.18' and make it public (but with 
a comment explaining why the old version is kept), just as in e.g. 
'python-flake8-2.2.4'.

Are you suggesting we keep bedtools-2.18 even if ribotaper updates to a 
newer version? I thought accepted practice was to delete old packages 
when they are no longer needed.

The patch LGTM otherwise, except that I would unpack 'ORF' and use the 
term 'ribo-seq' in the description. I've never looking at ribo-seq data 
before and I'm not familiar, so I wasn't sure what 'ribosome profiling' 
meant exactly e.g. is it measuring the amount of ribosome in a cell? I 
realise that isn't true, just illustrating the point. Perhaps I am too 
naive.

ben