Ben Woodcroft <b.woodcr...@uq.edu.au> writes:
>> 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.
No, I agree. We keep bedtools-2.18 as long as it’s needed for
Ribotaper.
> 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.
I don’t know how to naturally include the term “ribo-seq”, so how about
simply this:
Ribotaper is a method for defining translated @dfn{open reading
frames} (ORFs) using ribosome profiling (ribo-seq) data. This
package provides the Ribotaper pipeline.
Is this better?
~~ Ricardo
