[BioC] biomaRt question

[Dipl.-Ing. Johannes Rainer]

Hi Steffen,

thanks for your great support! i will wait for the new package...

thanks, jo


Quoting Steffen Durinck <sdurinck at ebi.ac.uk>:

> Hi Jo,
>
> In the function martConnect you should write something like this 
> (using the correct host,....)
>
> mart <- new("Mart",
>                ensembl = dbConnect(drv = driver,user = user, host = 
> host , dbname = databases$ensembl, password = password),
>                vega = dbConnect(drv = driver,user = user, host= host, 
> dbname = databases$vega, password = password),
>                sequence = dbConnect(drv = driver,user = user, host = 
> host, dbname = databases$sequence, password = password),
>                snp = dbConnect(drv = driver,user = user, host = host, 
> dbname = databases$snp, password = password),
>                arrayToSpecies = arrayToSpecies,
>                arrayToEnsembl = arrayToEnsembl
>                );
>
> You'll also need to change the host etc in the function listMarts
>
> listMarts <- function(host = "ensembldb.ensembl.org", user = 
> "anonymous", password = ""){
>
>  driv <- dbDriver("MySQL", force.reload = FALSE);
>  connection <- dbConnect(driv, user = user, host = host, password = 
> password);
>
>
> If you can wait a few more hours I could  send you the latest release 
> of biomaRt in which you don't have to make changes in the source code 
> anymore but can change host from within your R session.  BioMart 
> currently uses Ensembl_mart, snp_mart, vega_mart, and  sequence_mart. 
>  It will try to connect  to these marts all at  once.  We plan to 
> include a way of selection so if you only use ensembl you don't have 
> to install all other marts although these currently come together if 
> you do a local ensembl install.
>
> best,
> Steffen
>
>
>
> Dipl.-Ing. Johannes Rainer wrote:
>
>> hi,
>>
>> as i am behind a http proxy and the biomart package tries to 
>> establish a direct mysql connectioj to the ensembl database i had no 
>> chance to test or use the biomaRt package.
>> well, now i finally managed to install a local version of biomart 
>> (after some problems i had with different versions of mysql (i 
>> strongly recommend to use MySQL > 4.1 !)). my question is now, how 
>> and where do i have to change biomaRt source to connect to my local 
>> biomart database?
>> another question: which mart database uses biomaRt, i assume the 
>> ensemble_mart and not the uniprot and msd mart...
>>
>> cheers, jo
>>
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>
>