[Bioperl-l] loading data to biosql tables

[Angshu Kar]

Yes Jason. But what I've done is, instead of putting the .pm and .pl files
in default locations I've used the LIB and PREFIX arguments to place them in
my local directory. This I've done for bioperl as well as bioperl-db
modules.
Now could you please help me in how to make perl find it?

Thanks,
Angshu


On 12/10/05, Jason Stajich <jason.stajich at duke.edu> wrote:
>
> 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 <http://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
>
>
>
>