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Re: [PATCH] Add Ribotaper.

From: Ben Woodcroft
Subject: Re: [PATCH] Add Ribotaper.
Date: Sat, 9 Jul 2016 08:52:05 +1000
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Thunderbird/38.8.0

On 07/07/16 23:45, Ricardo Wurmus wrote:
Ben Woodcroft <address@hidden> 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there any difference from previous times we've had to include outdated
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

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.


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