[Bioperl-l] bptutorial.pl won't run

Philip M Terry pterry2 at unlnotes.unl.edu
Sun Mar 5 20:15:32 EST 2006


Would anyone be able to help with the following.

version of bioperl: Distribution    B/BI/BIRNEY/bioperl-1.4.tar.gz
platform: OS X 10.4.5
What trying to do: Install core bioperl modules, then run bptutorial.pl.
Code that gives the error: Following installation steps:

sudo perl -MCPAN -e shell;
cpan> install Bundle::CPAN
cpan> q
sudo perl -MCPAN -e shell;
cpan> install B/BI/BIRNEY/bioperl-1.4.tar.gz
cpan> q
sudo perl -MCPAN -e shell;
cpan> force install B/BI/BIRNEY/bioperl-1.4.tar.gz
cpan> q

Tried to run bptutorial.pl from its directory,

/opt/local/lib/perl5/site_perl/5.8.7 directory
Note: first changed two lines in bptutorial.pl

philip-terrys-power-mac-g5:/opt/local/lib/perl5/site_perl/5.8.7 mterry$
perl -w bptutorial.pl 1
Example 1 uses files in t/data
Directory t/data not found
philip-terrys-power-mac-g5:/opt/local/lib/perl5/site_perl/5.8.7 mterry$

Note: permissions are 444 for bptutorial.pl
Reset to 555, got same output, still won't run.

What to do to get bptutorial.pl to run on this system?

Philip M. Terry, Ph.D.
University of Nebraska-Lincoln

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