[Bioperl-l] loading data to biosql tables

[Jason Stajich]

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
>>>
>>
>>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12