[Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?

Dan Kortschak dan.kortschak at adelaide.edu.au
Tue Feb 9 15:51:55 EST 2010

Hi Rob,

Yes, I considered the problems involved in including B:A:IO:b in
bioperl-live because of that. Though I don't see it as a circularity
issue, just a straight dependency one.

>From memory (and a quick look at the .pm and .t files), in the absence
of bioperl-run the test should just be ignored (they currently are not
skipped - I will add that) and inclusion of the module in code should
fail informatively, so I don't really see that as a problem. If it is
seen as a problem though I think the best approach would be to migrate
it to bioperl-run, rather than placing it in it's own package -
bioperl-run already depends on bioperl-live, so all internal
dependencies would nominally be satisfied (samtools and other
executables are outside our control).

Other opinions?


On Tue, 2010-02-09 at 12:27 -0800, Robert Buels wrote:
> Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part 
> of bioperl-run.  Doesn't that introduce a circular dependency between 
> bioperl-live and bioperl-run?
> Perhaps it should be split out into its own CPAN distribution that 
> depends on both bioperl-run and bioperl-live?  Or maybe some way can be 
> found for it to not use Bio::Tools::Run::Samtools?
> Rob
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