[Bioperl-l] loading data to biosql tables

[Angshu Kar]

Thanks Chen. I'm running it on linux (red hat) too... but did you work with
biosql-db module and face that problem?

On 12/9/05, chen li <chen_li3 at yahoo.com> wrote:
>
> Based on my personal experience Bioperl is meant to
> run much much smoothly on linux system (or Unix).
> Which operation system are you using? If it is windows
> I expect you have a lot of troubles (now and in the
> future) for a novice even you install an ActivePerl. I
> have the same probelm before. But everything is fine
> after I install a red hat linxu Fedora core 1 on my
> computer.  Now I have dual OS on my computer. I follow
> the HOWTO INSTALL coming with Biosql and everything is
> fine.
>
> Li
>
> --- Angshu Kar <angshu96 at gmail.com> 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
> > >
> > >
> > >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> >
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
>