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

Sam Al-Droubi saldroubi at yahoo.com
Mon Mar 6 02:32:22 UTC 2006

  I am relatively new to Bioperl but I remember having problems installing it using CPAN so I installed it using make as described http://bioperl.open-bio.org/SRC/bioperl-live/INSTALL under section

  I installed version 1.5.1 and I completed an entire project with it without any problems.  I also remember installing the Bundle::Bioperl.  
  I think you should install the bundle first.  I also think it is ok to force the install since a few tests will fail with Bioperl but that's ok in most cases.   The book Mastering Perl for Bioinformatics talks about installing Bioperl if you have it. 
  You can get verion 1.5.1 from here  http://bioperl.org/DIST/ 
  The filename is bioperl-1.5.1.tar.gz
  Hope this helps. 

Philip M Terry <pterry2 at unlnotes.unl.edu> wrote:

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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Sam Al-Droubi, M.S.
saldroubi at yahoo.com

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