Hi Zhiliang,
The GMOD tutorial looks very complicated to me. It mixes 0.7 and 0.8
software, needs VM etc.
Installing and running 0.8 is much simpler, just follow the docs from 0.8.
Please start with section 4 on page 6 ("Quick Start"). If you can get it to
work, the next step is create an empty table in your database and populate
with a bit of data. Please follow section 5.4.1 on page 16. If you can do
that, then the next step is to create a 'real' table and populate it with
your 'real' data using a database import tool (e.g for mysql it is
mysqlimport) and repeat the procedure. If you having problems with
connecting to your database through MConfigurator, please use database
commandline tool running on the same host as MConfigurator to make sure
that you have sufficient privileges
a
On Wed, Dec 14, 2011 at 4:30 PM, Zhiliang <[email protected]> wrote:
> 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<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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