[Bioperl-l] how to tun bioperl and parsing blast report

[Brian Osborne]

Hank,

To run bptutorial.pl cd to the bioperl-1.2.3 directory in your home
directory, then try it.

You should also set your PERL5LIB environmental variable to that same
directory you specified in the make, so in csh or tcsh:

setenv PERL5LIB /home/dag/My_Local_Perl_Modules

I'm nor sure how to address your SearchIO questions. The SearchIO HOWTO
wasn't clear?


Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of hank wong
Sent: Monday, November 03, 2003 4:25 AM
To: bioperl-l at bioperl.org; bioperl-guts-l at bioperl.org
Subject: [Bioperl-l] how to tun bioperl and parsing blast report

Dear Sir, I tried to install Bioperl and make it work in my unix system. I
did not had the administrator mode, so I put everything in my writable
directary.

I followed these steps to install(go to the INSTALL):
 INSTALLING BIOPERL IN A PERSONAL OR PRIVATE MODULE AREA
 If you lack permission to install perl modules into the
 standard site_perl/ system area you can configure bioperl to
 install itself anywhere you choose. Ideally this would
 be a personal perl directory or standard place where you
 plan to put all your 'local' or personal perl modules.
 Note: you _must_ have write permission to this area.
 Simply pass a parameter to perl as it builds your system
 specific makefile.
 Example:
   perl Makefile.PL  PREFIX=/home/dag/My_Local_Perl_Modules
   make
   make test
   make install
---------------------------------------------------------
and get everything, here is the directary under my bioperl-1.2.3
AUTHORS     INSTALL.WIN     README            bioperl.lisp    examples
BUGS        LICENSE         biodatabases.PL   bioperl.pod     lib
Bio         LocalConfig.pm  biodatabases.pod  bioscripts.PL   models
Changes     MANIFEST.SKIP   biodesign.PL      bioscripts.pod  pm_to_blib
DEPRECATED  Makefile        biodesign.pod     blib            scripts
FAQ         Makefile.PL     bioperl.PL        bptutorial.pl   t
INSTALL     PLATFORMS       bioperl.conf      doc
-------------------
it seems everything is ok right now.
------------------------------------------------------

Here is my question, how to run Bioperl, and bptutorial.pl?
I tried like this:
>./bptutorial.pl
Can't locate IO/String.pm in @INC (@INC contains: .
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl) at
Bio/DB/WebDBSeqI.pm line 90.
BEGIN failed--compilation aborted at Bio/DB/WebDBSeqI.pm line 90.
Compilation failed in require at Bio/DB/DBFetch.pm line 75.
BEGIN failed--compilation aborted at Bio/DB/DBFetch.pm line 75.
Compilation failed in require at Bio/DB/EMBL.pm line 103.
BEGIN failed--compilation aborted at Bio/DB/EMBL.pm line 103.
Compilation failed in require at Bio/LiveSeq/IO/BioPerl.pm line 110.
BEGIN failed--compilation aborted at Bio/LiveSeq/IO/BioPerl.pm line 110.
Compilation failed in require at ./bptutorial.pl line 3730.
BEGIN failed--compilation aborted at ./bptutorial.pl line 3730.
----------------

And it got the above information. Do u think what way I can run
bptutorial.PL sucessfully?
2) I am typically very interested in the parsing blast report
which could use SearchIO modules...
I saw a Bio::SearchIO directary, but sounds I need to guidance to make it
run up.
Would you pls refer some FAQ page for guidance?
I tried the
page:
http://www.bioperl.org/Core/Latest/bptutorial.html#i.1_overview

http://bioperl.org/HOWTOs/html/SearchIO.html

anymore?
I appreciated your reply...

thanks,
-hank





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