[Bioperl-l] Packaging BioPerl for mandrake linux

[Guillaume Rousse]

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.
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