[Bio-packaging] testing out guix
ricardo.wurmus at mdc-berlin.de
Mon Jul 20 12:22:38 UTC 2015
Ben Woodcroft <b.woodcroft at uq.edu.au> writes:
> Is another option simply to ask the authors of the downstream tools
> whether their tool uses "coverage", and if so are they aware of the
> change? That way they get to find out too and update the software
> accordingly which is goodness beyond guix, as well as less work for us.
> There's only a few I think.
Sure, that’s an option. Personally, though, I’m reluctant to do this
unless a user asks for a particular version of a tool using “coverage”.
At the moment I prefer to consider this a problem of the authors of
“bedtools”, rather than my problem, because it doesn’t seem very
important, at least among the users for whom I’m packaging tools.
I guess this just shows that there is no general policy. Normally we
just update packages without much checking when new minor versions are
In this case, I see that there are only two packages using bedtools:
‘pybedtools’ and ‘clipper’ (which uses ‘pybedtools’). I do not know how
‘pybedtools’ works or if it is affected by the change. I guess it would
not be a bad idea to contact the authors of ‘pybedtools’ to ask. (Or
maybe there’s a more recent version of ‘pybedtools’?)
Personally, I would not worry too much about an update in this case. If
it breaks stuff we can always go back or patch.
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