[Bioperl-l] loading data to biosql tables

[Jason Stajich]

you have not installed it so that your perl knows to find it.  Did  
you do 'make install'?

On Dec 9, 2005, at 10:21 PM, Angshu Kar wrote:

> Thanks Jason...
> I'm sorry but I didn't get you.
> I've installed bioperl as well as bioperl-db module in my system...
> Now what should be my next step to resolve this problem?
> I'm sorry again, but as I told that I'm a novice in this domain.
>
> Thanks,
> Angshu
>
>
> On 12/9/05, Jason Stajich <jason.stajich at duke.edu> wrote:
>
> Follow the install instructions for bioperl first, you need bioperl
> to run bioperl-db.
> These include, set your PERL5LIB or install bioperl on your system or
> run the load script with -I PATH/TO/BIOPERL
>
>
> On Dec 9, 2005, at 7:54 PM, Angshu Kar wrote:
>
> > One thing I missed was that my Root.pm resides in a different
> > path...How to
> > specify that?
> >
> > On 12/9/05, Angshu Kar <angshu96 at gmail.com> wrote:
> >>
> >> Thanks a lot Barry.
> >>
> >> Now I'm getting this error while tryin to run the
> >> load_seqdatabase.pl in a
> >> linux box (I used :
> >> perl load_seqdatabase.pl /akar/seq/ATH1_cds_cm_20040228)
> >>
> >>
> >> Can't locate Bio/Root/Root.pm in @INC (@INC contains:
> >> /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5
> >> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
> >> /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi
> >> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi
> >> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi
> >> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi
> >> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
> >> /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4
> >> /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2
> >> /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0
> >> /usr/lib/perl5/site_perl
> >> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
> >> /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi
> >> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
> >> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi
> >> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi
> >> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
> >> /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4
> >> /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2
> >> /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0
> >> /usr/lib/perl5/vendor_perl .) at load_seqdatabase.pl line 7.
> >> BEGIN failed--compilation aborted at load_seqdatabase.pl line 7.
> >>
> >> Please guide.
> >>
> >> Thanks,
> >> Angshu
> >>
> >> On 12/9/05, Barry Moore < bmoore at genetics.utah.edu> wrote:
> >>>
> >>> Angshu-
> >>>
> >>> Make the namespace whatever you want it to be.  This is useful if
> >>> you
> >>> want to load sequence from different sources into the same
> >>> database.  As
> >>> for the format - you tell us what format is the file in?  You
> >>> could just
> >>> let bioperl guess, but looking at the file and deciding yourself
> >>> would
> >>> be your best bet.
> >>>
> >>> Barry
> >>>
> >>>> -----Original Message-----
> >>>> From: bioperl-l-bounces at portal.open-bio.org [mailto: bioperl-l-
> >>>> bounces at portal.open-bio.org] On Behalf Of Angshu Kar
> >>>> Sent: Friday, December 09, 2005 5:22 PM
> >>>> To: Sean Davis
> >>>> Cc: bioperl-l
> >>>> Subject: Re: [Bioperl-l] loading data to biosql tables
> >>>>
> >>>> Hi Sean,
> >>>>
> >>>> A small help I need before I run the load_seqdatabase.pl. I've
> >>> downloaded
> >>>> my
> >>>> datafile which is ATH1_cds_cm_20040228 from TAIR. What's the
> >>>> namespace
> >>>
> >>> and
> >>>> format for this?
> >>>>
> >>>> Thanks,
> >>>> Angshu
> >>>>
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at portal.open-bio.org
> >>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>
> >>
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
>

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12