[Bioperl-l] Bptutorial.pl

[Peter Schattner]

Hi Paul

Paul Boutros wrote:

> 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.

Thanks for finding this bug!  It should now be fixed in CVS.  Perhaps you
can try it again (since I don't have a Windows machine and am not sure that
my fix will work there)?

> 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>

This one is puzzling.  It should not be necessary (or IMO desirable) to turn
off warnings when running the tutorial.  I am unable to reproduce the error
on my Linux machine.  What version of StandAloneBlast.pm is the one in your
directory C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm?

Thanks

Peter