[Bioperl-l] loading data to biosql tables

[Brian Osborne]

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