[Bio-packaging] testing out guix

Ricardo Wurmus 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.

~~ Ricardo

More information about the bio-packaging mailing list