[Genquire-dev] Re: [Genquire-users] error installing LWP package

[David Block]

Hi Iry!

Genquire is still pretty young - we're definitely not at the 
./configure && make && make install stage yet.

Part of the problem is that it is both a gui and a database application.

One of our highest priorities is separating those two things.  The 
BioSQL schema will probably become the default database backend over 
time, but the default for now is rather homegrown.

Installing the gui is probably already done at your end.  However, the 
gui needs something to draw, and so you need to get a compatible 
database installation installed.  The one that comes with the install is 
pretty much ready to go, but it needs you to do the work yourself (sort 
of).

Once you have the database installed once, on a suitable, 
network-reachable server, the other installs of Genquire can just 
connect to that database and go from there.

So, you need to pick a good database server machine (Linux/Unix 
probably, OS X works :)

Then you need to make sure it has a fairly up-to-date installation of 
MySQL on it.

You need to get 'root' access to this installation.  This is different 
than root access to the machine.  You should be able to log in from the 
command line into the mysql client.

You should also test perl dbi installation, if possible.  Is DBD::Mysql 
installed properly?  That can be a real pain.

Then you can run Admin/init_db.pl.  That script simply instantiates the 
Genquire database schema for you, and does some initial data dumping.

Then the work begins :)

You have to install appropriate data!  That's a whole 'nother adventure!

OTOH, we'd love to see mouse annotations coming from Genquire!

Okay, sorry if I said too many obvious things.  Let us know where you're 
at, I'll try to check my mail regularly today and give you pointers.

Good Luck!

Dave (early on the West Coast)


On Friday, March 15, 2002, at 07:41  AM, Mark Wilkinson wrote:

> First:  please do clarify for us what OS you are using.
>
> Second:  check that you really can connect to the MySQL server 
> directly...
> if not, then deal with that first.
>
> Third:  ...  Over to you, Dave...  MySQL server issues are really not my
> bag...
>
> Mark
>
>
>
> Iry Witham wrote:
>
>>> Mark,
>>
>>         I have done this and get an error message that says:
>>
>> 'failed to connect to mySQL server: Can't connect to MySQL server on
>> localhost <10061>  This will not work unless we can get root access
>> to the database.  Please correct the above errors and try again.'
>>
>> Why do I get this error?
>>
>> Iry
>>
>>> Dave, correct me if I am wrong:
>>>
>>> the script is in the Admin folder.  It is called   init_db.pl
>>>
>>> M
>>>
>>>
>>> Iry Witham wrote:
>>>
>>>>  Good Morning,
>>>>
>>>>          I am at the point of installing Genquire and the 
>>>> instructions
>>>>  tell me that if I plan to run a local database I must be the MySQL
>>>>  root user.  It says to unpack the files into my final working
>>>>  directory and run the install script.  The problem is, What is the
>>>>  file name for the install script?
>>>>
>>>>  Thanks,
>>>>
>>>>  Iry
>>>>  --
>>>>  Iry T. Witham
>>>>  Technical Support Specialist
>>>>  Mouse Genome Informatics
>>>>  The Jackson Laboratory
>>>>  600 Main Street
>>>>  Bar Harbor, ME 04609
>>>>
>>>>  Phone:  (207)288-6744
>>>>  Fax:    (207)288-6131
>>>>  E-mail: itw@informatics.jax.org
>>>>          iwitham@mac.com
>>>>  _______________________________________________
>>>>  Genquire-users maillist  -  Genquire-users@bioinformatics.org
>>>>  http://bioinformatics.org/mailman/listinfo/genquire-users
>>>
>>> --
>>> --------------------------------
>>> "Speed is subsittute fo accurancy."
>>> ________________________________
>>>
>>> Dr. Mark Wilkinson
>>> Bioinformatics Group
>>> National Research Council of Canada
>>> Plant Biotechnology Institute
>>> 110 Gymnasium Place
>>> Saskatoon, SK
>>> Canada
>>
>> --
>> Iry T. Witham
>> Technical Support Specialist
>> Mouse Genome Informatics
>> The Jackson Laboratory
>> 600 Main Street
>> Bar Harbor, ME 04609
>>
>> Phone:  (207)288-6744
>> Fax:    (207)288-6131
>> E-mail: itw@informatics.jax.org
>>         iwitham@mac.com
>
> --
> --------------------------------
> "Speed is subsittute fo accurancy."
> ________________________________
>
> Dr. Mark Wilkinson
> Bioinformatics Group
> National Research Council of Canada
> Plant Biotechnology Institute
> 110 Gymnasium Place
> Saskatoon, SK
> Canada
>
>
>
> _______________________________________________
> Genquire-dev maillist  -  Genquire-dev@bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/genquire-dev
>
>
--
David Block          (858)812-1513
Bioinformatics        http://www.gnf.org
dblock@gnf.org        Just ridin' the Coaster...