[Bioperl-l] loading data to biosql tables

Angshu Kar angshu96 at gmail.com
Sat Dec 10 12:17:09 EST 2005 

You are marvellous Jason...Thanks a lot for using the lingo thats for a
freshie like me.
I'll apply this today to the load_seqdatabase.pl and let you know if any
problem arises.

Thanks,
Angshu


On 12/10/05, Jason Stajich <jason.stajich at duke.edu> wrote:
>
>  From the INSTALL document in the Bioperl distribution
>
>
>    You can explicitly tell perl where to look for modules by using the
>    lib module which comes standard with perl.
>
>
>    Example:
>
>
>        #!/usr/bin/perl
>
>
>        use lib "/home/users/dag/My_Local_Perl_Modules/";
>        use Bio::Seq;
>
>
>        <...insert whizzy perl code here...>
>
>
>    Or, you can set the environmental variable PERL5LIB:
>
>
>      csh or tcsh:
>
>
>        setenv PERL5LIB /home/users/dag/My_Local_Perl_Modules/
>
>      bash or sh:
>
>
>       export PERL5LIB=/home/users/dag/My_Local_Perl_Modules/
>
>
>
>  On Dec 10, 2005, at 11:51 AM, Angshu Kar wrote:
>
>  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
> >
> >
> >
> >
>
>
>  --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
>
>

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