[Bioperl-l] bioperl-db and MySQL

[Hilmar Lapp]

On Nov 17, 2005, at 1:24 PM, chen li wrote:

> Hi Hilmar,
>
> I ran "make test" but it still failed.

Please post the error message; generally it should not fail.

>  But I were able
> to create a biosql instance within MySQL (same as
> those described in mysql HOWTO) after I loaded the
> schema of seqdatabase.spl. So I think I might succeed
> in installing Bioperl-db.  Now I want to go to the
> next step: loading a test EST database file(fasta
> format)into the database. I already download the mouse
> EEST, unzip  the file, and put it as
> c:/perl/EST/est_mouse( and
> C:/bioperl-db-0.1/scripts/load_seqdatabase.pl).

This looks like you are using the old 0.1 release. You will need a 
post-Capetown/pre-Singapore BioSQL schema in order for this to work - 
the current download from CVS will *not* work with this release.

I recommend you use a CVS download for both the BioSQL schema and 
Bioperl-db, using the main trunk in both cases.

> By
> following HOWTO I am supposed to the use syntax below
> to load the file into databse.
>
> ./load_seqdatabase.pl <options> <dataset identifier>
> /path/to/data/file(s)
>
> My questions: in which windows should I type this line
> of command, mysql,Perl,or the directory containing
> load_seqdatabase.pl?

Given that you are calling the script as sitting in the current 
directory, that's where you should be ... Generally speaking you can 
call it from anywhere though, just give the full location.

	-hilmar

>   And how do I issue the command
> in this specific case?
>
> Thanks,
>
> Li
>
>
>
>
>
> --- Hilmar Lapp <hlapp at gmx.net> wrote:
>
>> You run 'make test' to see if it works. Installation
>> itself can't
>> really get much wrong.
>>
>> You need to follow the instructions for
>> t/DBHarness.conf.example before
>> you can successfully run 'make test'.
>>
>> 	-hilmar
>>
>> On Nov 16, 2005, at 3:53 PM, chen li wrote:
>>
>>> I unzipped the download files and used "nmake
>> install"
>>> to install bioperl-db on my computer. And it seems
>> it
>>> works because I see many files/pm are copied to
>> the
>>> defautl library(c:/Perl/site/lib/Bio/DB...." on my
>>> computer). Now my question: How do I know if it is
>>> installed correctly and will be working? Can I
>> issue a
>>> command like "perldoc ???" to check if it is in
>> the
>>> documantation?
>>>
>>> Thanks,
>>>
>>> Li
>>>
>>> --- Hilmar Lapp <hlapp at gmx.net> wrote:
>>>
>>>> Bioperl-db needs to be in your @INC (perl's path
>> for
>>>> loading perl
>>>> modules) at runtime - so it doesn't matter where
>> you
>>>> put it so long as
>>>> you have the location in the PERL5LIB environment
>>>> variable before
>>>> executing a script, or include the location at
>> the
>>>> top of the script
>>>> via 'use lib c:\path\to\bioperl-db;'. Supposedly,
>>>> simply installing
>>>> bioperl-db should take care of the problem too.
>>>>
>>>> 	-hilmar
>>>>
>>>> On Nov 5, 2005, at 5:20 PM, chen li wrote:
>>>>
>>>>> Hello everyone,
>>>>>
>>>>> I want to install bioperl-db on my windows XP
>> with
>>>>> ActivePerl.  I read the HOWTOs about installing(
>>>>>
>>>>
>>>
>>
> http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/docs/
>>>>
>>>>> HOWTO-MySQL.html).
>>>>> But I failed to do the nmake test. Then I read
>> the
>>>>> HOWTOs again, which points out that install will
>>>> fail
>>>>> if the DBD:: and DBI::Mysql modules cannot be
>>>> found.
>>>>>
>>>>> On my PC MySQL, Perl, and Bioperl-db are kept in
>>>>> different directory. I use PPM to install
>>>> DBD::Mysql
>>>>> and DBI::Mysql. I install MySQL using binary
>> code.
>>>> My
>>>>> question: Where should I keep the Bioperl-db
>>>> including
>>>>> bioperl-schema so that installation will
>> succeed?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Li
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 	
>>>>> 		
>>>>> __________________________________
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>>>>> http://mail.yahoo.com
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at portal.open-bio.org
>>>>>
>>>>
>>>
>>
> 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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>>>
>> -- 
>>
> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp
>> at gnf.org
>> GNF, San Diego, Ca. 92121              phone:
>> +1-858-812-1757
>>
> -------------------------------------------------------------
>>
>>
>>
>
>
>
> 		
> __________________________________
> Yahoo! FareChase: Search multiple travel sites in one click.
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>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------