[Bioperl-l] Questions on SEALS from NCBI

[Leonardo Marino-Ramirez]

SEALS is a great package but it needs to be updated. Here are some ways
around it:

builtin has been replaced by the Scalar-List-Utils distribution and
is no longer avaliable.

You can get Scalar-List-Utils from my CPAN directory
http://www.perl.com/CPAN/authors/id/GBARR/

Just edit the files that use builtin and replace it with the
Scalar-List-Utils module instead.

Regards, Leonardo

On Wed, 13 Jun 2001, LIQING ZHANG wrote:

> Hello,
>
> I downloaded the SEALS package from NCBI and have been trying to get it
> work on my red-hat linux mechanine.  But I got some problems. Some
> commands such as blast2gi, blast2filename, all commands under splish and
> splat do not work, while others like formatdb, blastall work.  When I
> typed in blast2gi, for example, it gave the following:
>
> blast2gi   (supposedly, this should give me the man page of this
> command)
> I got this:
> Can't locate builtin.pm in @INC (@INC contains:
> /home/liqing/SEALS/seals/bin/../
> lib/perl/alpha-linux /home/liqing/SEALS/seals/bin/../lib/perl
> /home/liqing/SEALS
> /seals/lib/perl/alpha-linux /home/liqing/SEALS/seals/lib/perl
> /usr/lib/perl5/5.0
> 0503/alpha-linux /usr/lib/perl5/5.00503
> /usr/lib/perl5/site_perl/5.005/alpha-lin
> ux /usr/lib/perl5/site_perl/5.005 .) at
> /home/liqing/SEALS/seals/bin/blast2gi li
> ne 211.
> BEGIN failed--compilation aborted at
> /home/liqing/SEALS/seals/bin/blast2gi line
> 211.
>
> I thought that this is due to failure of installation of some perl
> modules, but it seems that there are some more besides builtin.pm.
>
> So my first question is: how can I find out which pm required for SEALS
> is installed, which is not?
> My second question is: I tried to install builtin.pm from cpan, but only
> found a builtins, can anyone tell me what is the right module to
> install, how and where i install it to?
>
> Many thanks in advance,
> Liqing
> lzhang@uci.edu
> Eco. evol biol dept.
>
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-- 

___ _/ ________________________________________________________________
   _/
  _/    _/      _/_/_/    Leonardo Marino-Ramirez  marino@tofu.tamu.edu
 _/    _/_/  _/_/    _/  Biochemistry Department, Texas A&M University
_/_/_/_/  _/  _/_/_/    2128 TAMU, College Station, TX 77802-2128, USA
     _/      _/     _/ Voice: (979) 862-4055   Fax: (979) 845-9274
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