[Bioperl-l] Packaging BioPerl for mandrake linux

Guillaume Rousse rousse at ccr.jussieu.fr
Fri Jan 9 18:13:26 EST 2004

On Friday 09 January 2004 23:47, Guillaume Rousse wrote:
> > > This make both packages to requires each other. Maybe those modules
> > > should be
> > > moved to bioperl-run, to make bioperl self-sufficient ?
> >
> > bioperl-run requires bioperl, period.  bioperl makes use of many
> > "external" packages, but they are mostly optional (required only for a
> > very small subset of bioperl functionality).  In general, we'd like
> > people to be able to install the core BioPerl without a ton of other
> > packages (and certainly without requiring bioperl-run).  All bioperl
> > tests should pass (i.e. be skipped, if necessary) without bioperl-run
> > installed (is that not true?)
> Right.
> Those dependencies are generated by rpm automatic dependencies computing,
> because they are some files in bioperl triggering them. A quick grep shows
> the included scripts are responsable:
> blast2tree.pl:use Bio::Tools::Run::Phylo::Molphy::ProtML
> clustalw.pl:use Bio::Tools::Run::Alignment::Clustalw;
> I'll silent them manually.
Acutallly not.

The following scripts from bioperl core won't work if bioperl-run is not 
So they should belong to bioperl-run tarball instead.
The number of horses you own increases according to the number of stalls in 
your barn
		-- Murphy's Horse Laws n°13

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