[Bioperl-l] Re: Regarding the Bioperl-db you installed..

[Damien Mattei]

Hello,

a few month ago i set up an SQL database using the Chris howto,
i was using redhat7.2, mySQL  3.23.41, bioperl 1.0 and i had really few 
problem and was very happy of this Howto. The version of bioper-db i 
used was bioperl-db-0.1.tar.gz.
I can send you this version of bioperl-db if you want, but as far as i 
can remember the problems can be in the script that create the database 
tables or after when loading/retrieving sequence from database.
Did you succeed in creating first the database?
Give us some error output if you want to be help,it's hard to answer 
with few informations.

Best Regards,

Damien

Chris Dagdigian wrote:
> 
> Hi Andrew,
> 
> My BioSQL howto/install diary document is out of date with respect to 
> the current codebases for both bioperl-db and biosql. Updating that 
> document is high on my to-do list as I need to get some MacOS X specific 
> pointers in there.
> 
> I'm cc'ing this reply to both the biosql and bioperl mailing lists to 
> see if anyone else can answer your specific questions. I'm no longer 
> sure if people should be downloading the live branch from CVS or some 
> tagged version instead.
> 
> Any feedback from you on how to improve the document would greatly be 
> appreciated
> 
> Regards,
> Chris
> 
> 
> Dr. Andrew Michael Lynn wrote:
> 
>> Hi,  
>> I run a course where I am trying to get our students acquainted with 
>> Bioperl. In order to make things more exciting, we attempted to setup 
>> a core server system with Apache, bioperl and wanted to have an SQL 
>> backend. I noticed your HOWTO on setting up MyGenBank ... we cannot 
>> set up the bioperl-db, possibly because of conflicts between versions. 
>> I note from the biosql newsgroup that the head of the CVS should not 
>> be used but the branch tagged bioperl-1-1 is stable. I cannot get this 
>> to run as well - there are SQL errors. Can you tell me the versions 
>> of  1. Bioperl 2. MySQL 3. Bioperl-db/biosql you used?  
>> I have bioperl 1.0.2, MySQL 3.23.49-3 (Redhat 7.3) and  various 
>> versions of bioperl-db.  
>> We will be glad to help in writing the HOWTO's.  
>> With regards, Andrew Lynn  
>> __________________________________________________ Andrew Lynn, Ph.D 
>> Assistant Professor, Bioinformatics Centre. School of Information 
>> Technology, Jawaharlal Nehru University (http://www.jnu.ac.in) New 
>> Delhi - 110 067, India 
> 
> 
> 
> 


-- 
----------------------------
Damien Mattei
C.N.R.S / U.N.S.A - UMR 6549
mailto:mattei@unice.fr
http://www-iag.unice.fr/
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