[Bioperl-l] loading data to biosql tables

[Angshu Kar]

Hi Brian,

That sounds great! But in our labs they don't have any win boxes! Could
you please let me know how to get my problem resolved in a linux box?

Thanks,
Angshu


On 12/10/05, Brian Osborne <osborne1 at optonline.net> wrote:
>
> Li,
>
> Cygwin on Windows is a great platform for Bioperl, I used it happily for
> many years. When I was using Windows and Cygwin I recall getting
> bioperl-db
> and Biosql up and running in 10 minutes using the postgres package from
> Cygwin, and this was the first time I tried to install bioperl-db and
> Biosql
> with postgres. Since Cygwin is a Unix emulator all the INSTALL
> instructions
> work perfectly without any amendments.
>
> Brian O.
>
>
> On 12/9/05 11:46 PM, "Angshu Kar" <angshu96 at gmail.com> wrote:
>
> > 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
> >>>>
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
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> >>>
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> >>>
> >>
> >>
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