[Bioperl-l] loading data to biosql tables

Angshu Kar angshu96 at gmail.com
Sat Dec 10 17:59:19 EST 2005 

Hi,

Now I'm getting this new error:

Can't locate Bio/DB/BioDB.pm in @INC (@INC contains:
/home/akar/local/perl//i386-linux-thread-multi /home/akar/local/perl/
/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 8.
BEGIN failed--compilation aborted at load_seqdatabase.pl line 8.


I've checked the Bio/DB/ folder but it doesn't contain the BioDB.pm module -
it contains the following:


Ace.pm       DBFetch.pm    Flat        GFF               MeSH.pm
RefSeq.pm     Taxonomy.pm        XEMBLService.pm
Biblio       EMBL.pm       Flat.pm     GFF.pm            NCBIHelper.pm
Registry.pm   Universal.pm
BiblioI.pm   Failover.pm   GDB.pm      InMemoryCache.pm  Query
SeqI.pm       UpdateableSeqI.pm
BioFetch.pm  Fasta.pm      GenBank.pm  Makefile.PL       QueryI.pm
SwissProt.pm  WebDBSeqI.pm
CUTG.pm      FileCache.pm  GenPept.pm  MANIFEST          RandomAccessI.pm
Taxonomy      XEMBL.pm

Have I installed some wrong version of bioperl-db ? (I've used
http://bio.perl.org/Core/Latest/index.shtml)

Could anyone please let me know what I've missed?

Thanks,
Angshu


On 12/10/05, Angshu Kar <angshu96 at gmail.com> wrote:
>
> 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 <http://www.duke.edu/%7Ejes12>
> > > >
> > > >
> > > >
> > >
> > >  --
> > > Jason Stajich
> > > Duke University
> > > http://www.duke.edu/~jes12 <http://www.duke.edu/%7Ejes12>
> > >
> > >
> > >
> > >
> >
> >
> >  --
> > Jason Stajich
> > Duke University
> > http://www.duke.edu/~jes12 <http://www.duke.edu/%7Ejes12>
> >
> >
> >
> >
>
>

More information about the Bioperl-l mailing list