Hi Arek,
Thank you for your quick reply. I suppose your "MConfigurator" refers to
"scripts/martconfigurator.sh" on the local installation. I did a test and
now have a feel how to get my MySQL to it.
(It sees all my other databases besides the one I wish to give to it.
A quick question: what's the biomart's user agent name on a local system
that can be granted an access to a database on my MySQL?
(I started the biomart on my user account and it runs with my uid).
I found this tutorial useful - http://gmod.org/wiki/BioMart_Tutorial
It could be better if it comes with a simple sample data set to scroll
along :) I am still trying to close the gap between my flat map data file
and ... a mart db. It's interesting the tutorial says it can build mart
schema. I have not found how the keys between (supposedly my custom)
tables are recognized...
Best regards,
Zhiliang
On Wed, 14 Dec 2011, Arek Kasprzyk wrote:
Date: Wed, 14 Dec 2011 10:42:39 -0500
From: Arek Kasprzyk <[email protected]>
To: Zhiliang <[email protected]>
Cc: [email protected]
Subject: Re: [BioMart Users] format and load own data into Biomart?
Hi Zhiliang,
It does not really matter how you load data into BioMart as long as it ends
up in a relational database containing BioMart schema. You can therefore
use standard loading approaches e.g. the data import tools that come with
the database and then use MConfigurator tool to configure it. If you
already have a relational database that you are trying to convert to
BioMart spec, you can use the MConfigurator tool to do it for you.
My favourite approach to quickly learning how to set up a BioMart database
is to simply create a database with one table and a few rows of data on
your laptop and then configure it with MConfigurator and launch the server
there. It will give you an immediate feel how the software works
a
On Wed, Dec 14, 2011 at 10:17 AM, Zhiliang <[email protected]> wrote:
Maybe I was not careful enough but by scanning through Biomart user manual
and online tutorial I don't seem to find how to build own data sets into a
local Biomart install. We wish to share some large sets of own mapping
data with Biomart among our consortium members. Any hint on steps/tools to
format, load and configure own data is appreciated.
Thank you,
Zhiliang
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