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

[Hilmar Lapp]

Use branches bioperl-release-1-1-0 across the board. For bioperl this is the 1.1.0 developer's release (I'm not sure the 1.0.x series will work, but can't recall specific KO facts). Later versions of bioperl-live (e.g. the 1.1.1 developer's release) may work (should work, but it's not been tested by anyone AFAIK).

In order to use the main trunk versions, you'd need to upgrade your MySQL and you need the latest version of bioperl-live. You'd have to regularly update your checkout to sync with bug-fixes. Unless you enjoy living on the bleeding edge, you don't want to do that. (Having said that I can't refrain though from stating that the main trunk *is* workable.)

If you want us to be of more help you need to send the error message and possibly the circumstance or better yet script and input that leads to the error.

	-hilmar
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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> -----Original Message-----
> From: Chris Dagdigian [mailto:dag@sonsorol.org]
> Sent: Friday, October 25, 2002 7:31 AM
> To: Dr. Andrew Michael Lynn
> Cc: biosql-l@open-bio.org; bioperl-l@bioperl.org
> Subject: [BioSQL-l] Re: Regarding the Bioperl-db you installed..
> 
> 
> 
> 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 My BioSQL howto/install diary document is out of date with respect to 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 
> 
> 
> 
> -- 
> Chris Dagdigian, <dag@sonsorol.org>
> Independent life science IT & research computing consulting
> Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
> Work: http://BioTeam.net PGP KeyID: 83D4310E  Yahoo IM: craffi
> 
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