Re: [PATCH] Add Ribotaper.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

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 there any difference from previous times we've had to include outdated 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.

> Note that I just updated bedtools, although I imagine that won't help here.

No, the format hasn’t changed back.  Ribotaper was not developed with
the more recent versions, which all output more columns.

~~ Ricardo