[Bioperl-l] bioperl-db and MySQL

[chen li]

Hi Hilmar,

I ran "make test" but it still failed. But I were able
to create a biosql instance within MySQL (same as 
those described in mysql HOWTO) after I loaded the
schema of seqdatabase.spl. So I think I might succeed
in installing Bioperl-db.  Now I want to go to the
next step: loading a test EST database file(fasta
format)into the database. I already download the mouse
EEST, unzip  the file, and put it as
c:/perl/EST/est_mouse( and
C:/bioperl-db-0.1/scripts/load_seqdatabase.pl). By
following HOWTO I am supposed to the use syntax below
to load the file into databse.

./load_seqdatabase.pl <options> <dataset identifier>
/path/to/data/file(s)

My questions: in which windows should I type this line
of command, mysql,Perl,or the directory containing
load_seqdatabase.pl?  And how do I issue the command
in this specific case?

Thanks,

Li 

 



--- Hilmar Lapp <hlapp at gmx.net> wrote:

> You run 'make test' to see if it works. Installation
> itself can't 
> really get much wrong.
> 
> You need to follow the instructions for
> t/DBHarness.conf.example before 
> you can successfully run 'make test'.
> 
> 	-hilmar
> 
> On Nov 16, 2005, at 3:53 PM, chen li wrote:
> 
> > I unzipped the download files and used "nmake
> install"
> > to install bioperl-db on my computer. And it seems
> it
> > works because I see many files/pm are copied to
> the
> > defautl library(c:/Perl/site/lib/Bio/DB...." on my
> > computer). Now my question: How do I know if it is
> > installed correctly and will be working? Can I
> issue a
> > command like "perldoc ???" to check if it is in
> the
> > documantation?
> >
> > Thanks,
> >
> > Li
> >
> > --- Hilmar Lapp <hlapp at gmx.net> wrote:
> >
> >> Bioperl-db needs to be in your @INC (perl's path
> for
> >> loading perl
> >> modules) at runtime - so it doesn't matter where
> you
> >> put it so long as
> >> you have the location in the PERL5LIB environment
> >> variable before
> >> executing a script, or include the location at
> the
> >> top of the script
> >> via 'use lib c:\path\to\bioperl-db;'. Supposedly,
> >> simply installing
> >> bioperl-db should take care of the problem too.
> >>
> >> 	-hilmar
> >>
> >> On Nov 5, 2005, at 5:20 PM, chen li wrote:
> >>
> >>> Hello everyone,
> >>>
> >>> I want to install bioperl-db on my windows XP
> with
> >>> ActivePerl.  I read the HOWTOs about installing(
> >>>
> >>
> >
>
http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/docs/
> >>
> >>> HOWTO-MySQL.html).
> >>> But I failed to do the nmake test. Then I read
> the
> >>> HOWTOs again, which points out that install will
> >> fail
> >>> if the DBD:: and DBI::Mysql modules cannot be
> >> found.
> >>>
> >>> On my PC MySQL, Perl, and Bioperl-db are kept in
> >>> different directory. I use PPM to install
> >> DBD::Mysql
> >>> and DBI::Mysql. I install MySQL using binary
> code.
> >> My
> >>> question: Where should I keep the Bioperl-db
> >> including
> >>> bioperl-schema so that installation will
> succeed?
> >>>
> >>> Thanks,
> >>>
> >>> Li
> >>>
> >>>
> >>>
> >>>
> >>> 	
> >>> 		
> >>> __________________________________
> >>> Yahoo! Mail - PC Magazine Editors' Choice 2005
> >>> http://mail.yahoo.com
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at portal.open-bio.org
> >>>
> >>
> >
>
http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >> -- 
> >>
> >
>
-------------------------------------------------------------
> >> Hilmar Lapp                            email:
> lapp
> >> at gnf.org
> >> GNF, San Diego, Ca. 92121              phone:
> >> +1-858-812-1757
> >>
> >
>
-------------------------------------------------------------
> >>
> >>
> >>
> >
> >
> >
> > 		
> > __________________________________
> > Yahoo! FareChase: Search multiple travel sites in
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> >
> -- 
>
-------------------------------------------------------------
> Hilmar Lapp                            email: lapp
> at gnf.org
> GNF, San Diego, Ca. 92121              phone:
> +1-858-812-1757
>
-------------------------------------------------------------
> 
> 
> 



		
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