[Bioperl-l] Packaging BioPerl for mandrake linux

[Jason Stajich]

We're probably not going to move them out of that scripts dir in
bioperl-core but if you want to remove them from the -core rpm you are
building feel free.

There is a scripts dir in bioperl-run but as aaron said it isn't that
mature so I would rather aggregate mature scripts in one place rather than
having people play 'find the script'.

If you are really concerned about this just combine bioperl-core and
bioperl-run into on RPM I guess although we've not been religous about
making sure there are no duplicate filenames in both script dirs.


-jason

On Sat, 10 Jan 2004, Guillaume Rousse wrote:

> I've sent this mail before completing it :-(
>
> On Saturday 10 January 2004 01:31, Guillaume Rousse wrote:
> > On Saturday 10 January 2004 01:18, Aaron J.Mackey wrote:
> > > How about we make them "run" (i.e. die with a pleasant error message
> > > telling you to install bioperl-run to make use of these scripts)? ...
> >
> > That is what they already do, at least for bp_pairwise_kaks.pl:
> >
> > eval {
> >     # Ka/Ks estimators
> >     require Bio::Tools::Run::Phylo::PAML::Codeml;
> >     require Bio::Tools::Run::Phylo::PAML::Yn00;
> >
> >     # Multiple Sequence Alignment programs
> >     require Bio::Tools::Run::Alignment::Clustalw;
> >     require Bio::Tools::Run::Alignment::TCoffee;
> > };
> > if( $@ ) {
> >     die("Must have bioperl-run pkg installed to run this script");
> > }
> >
> > but not blast2tree.pl:
> > use Bio::Tools::Run::Alignment::Clustalw;
> > use Bio::Tools::Run::Phylo::Phylip::ProtDist;
> > use Bio::Tools::Run::Phylo::Phylip::Neighbor;
> > use Bio::Tools::Run::Phylo::Molphy::ProtML;
> > use Bio::Tools::Run::Phylo::Phylip::ProtPars;
>
> ... But from a strict packaging point of view, it is useless to install
> scripts that are bound to fail.
>
> > > our "scripts" support in bioperl-run isn't as mature as it is in main
> > > bioperl (opportunity for someone to Make A Difference, here).
> I guess you mean installation support in Makefile.PL ? Otherwise, i see no
> problem adding a script directory in bioperl-run tarball.
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu