[Bioperl-l] problem with Bio::Tools::EMBOSS

[Dave Messina]

Hi Anjan,

Bio::Factory::EMBOSS is not part of the BioPerl core distribution, but
rather part of bioperl-run. For some reason CPAN went for the old (1.4)
version of bioperl-run rather than the current 1.5.2.

And indeed, I seem to run into the same problem:
cpan> d /bioperl/

Distribution    BIRNEY/bioperl-1.2.1.tar.gz
Distribution    BIRNEY/bioperl-1.2.2.tar.gz
Distribution    BIRNEY/bioperl-1.2.3.tar.gz
Distribution    BIRNEY/bioperl-1.2.tar.gz
Distribution    BIRNEY/bioperl-1.4.tar.gz
Distribution    BIRNEY/bioperl-db-0.1.tar.gz
Distribution    BIRNEY/bioperl-ext-1.4.tar.gz
Distribution    BIRNEY/bioperl-gui-0.7.tar.gz
Distribution    BIRNEY/bioperl-run-1.2.2.tar.gz
Distribution    BIRNEY/bioperl-run-1.4.tar.gz
Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
12 items found

but when I ask in a different way the right distributions show up. [Sendu,
any idea what's going on here?]

cpan> ls
SENDU
 5919092 2007-02-14 SENDU/bioperl-1.5.2_102.tar.gz
  320154 2006-12-06 SENDU/bioperl-db-1.5.2_100.tar.gz
   99082 2006-12-06 SENDU/bioperl-network-1.5.2_100.tar.gz
  942093 2006-12-06 SENDU/bioperl-run-1.5.2_100.tar.gz

So try doing

cpan> install SENDU/bioperl-run-1.5.2_100.tar.gz

Or if CPAN refuses to cooperate, you can grab it from here:
http://www.bioperl.org/wiki/Getting_BioPerl#Bioperl_1.5.2.2C_Developer_Release


Dave