[Bioperl-l] Packaging BioPerl for mandrake linux

Guillaume Rousse rousse at ccr.jussieu.fr
Fri Jan 9 19:31:42 EST 2004

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;

> our "scripts" support in bioperl-run isn't as mature as it is in main
> bioperl (opportunity for someone to Make A Difference, here).

Propane/butane tanks that are full when they are packed, will unexplainably 
empty themselves before you can reach the campsite
		-- Murphy's Laws of Camping n°12

More information about the Bioperl-l mailing list