[Bioperl-l] loading data to biosql tables

Hilmar Lapp hlapp at gmx.net
Sat Dec 10 21:51:57 EST 2005 

Well this means that the place where you installed Bioperl-db is  
different from the one you installed Bioperl, and you didn't include it  
in your PERL5LIB setting. You can have multiple directories in  
PERL5LIB, separate them by colon:

	$ setenv PERL5LIB  
/path/to/where/I/installed/bioperl:/path/to/where/I/installed/bioperl- 
db

-hilmar

On Dec 10, 2005, at 2:59 PM, Angshu Kar wrote:

> 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>
>>>
>>>
>>>
>>>
>>
>>
>
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> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

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