[Bioperl-l] Bptutorial.pl

[Paul Boutros]

Just tried to run the tutorial on:
PERL 5.6.1
WinXP SP1

c:\perl\bioperl-live> perl -c bptutorial.pl
Can't locate Bio/Tools/Run/Alignment/TCoffee.pm in @INC (@INC contains: .
C:/Perl/lib C:/Perl/site/lib) at bptutorial.pl line 3118.
BEGIN failed--compilation aborted at bptutorial.pl line 3118.

Which is of course true: I don't have bioperl-run loaded on this machine.
When I loaded bioperl-run it does compile cleanly.  I'm not sure if this
would be an issue or not.

If I run it as:
c:\perl\bioperl-live> perl bptutorial.pl 0
all works properly

And if I run it as:
c:\perl\bioperl-live> perl bptutorial.pl 0
I get the usual subroutine redefinition warnings as well as:

Can't use string ("Bio::Tools::Run::StandAloneBlast") as a HASH ref
while "strict refs" in use at
C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm line 366. 

Based on the subroutine redefinitions, I would suggest that the running
instructions in bptutorial are changed from:
perl -w bptutorial.pl <parameters>
to just:
perl bptutorial.pl <parameters>