How to enable Multiple databases on Biomart?

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suo
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How to enable Multiple databases on Biomart?

suo
Dear All,

How to put multiple databases in the registry file or make other configuration to make it happen?

In the manual, a registry file is like:

<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE MartRegistry>
 <MartRegistry>
   <MartDBLocation
          name         = "my_mart"
          displayName  = "My BioMart Database"
          databaseType = "mysql"
          host         = "localhost"
          port         = "3306"
          database     = "my_mart"
          schema       = "my_mart"
          user         = "gmod"
          password     = "gmod"
          visible      = "1"
          default      = ""
          includeDatasets = ""
          martUser     = ""
   />
 </MartRegistry>

Thanks in advance!





     
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Re: How to enable Multiple databases on Biomart?

Darren Oakley
Hi,

Just add in extra 'MartDBLocation' or 'MartURLLocation' blocks to the XML.  Here's a small portion of one of ours:

<!DOCTYPE MartRegistry>
<MartRegistry>
   <MartDBLocation 
       name            = "ikmc" 
       displayName     = "IKMC Genes and Products" 
       databaseType    = "mysql" 
       host            = "xxxx.internal.sanger.ac.uk" 
       port            = "3303" 
       database        = "ikmc_mart_alt" 
       schema          = "ikmc_mart_alt" 
       user            = "xxxx" 
       password        = "xxxx" 
       visible         = "1" 
       default         = "" 
       includeDatasets = "" 
       martUser        = ""
   />
   <MartURLLocation 
     name                = "biomart"
     database            = "biomart" 
     default             = ""
     displayName         = "MGI (Jackson Laboratory US)"
     host                = "www.biomart.org"
     proxy               = "http://wwwcache.sanger.ac.uk:3128"
     includeDatasets     = "markers"
     martUser            = "" 
     path                = "/biomart/martservice"
     port                = "80"
     serverVirtualSchema = "default"
     visible             = "1"
   />
   <MartURLLocation 
     name                = "htgt" 
     database            = "htgt_mart" 
     default             = "" 
     displayName         = "WTSI Mouse Genetics Programme (Sanger UK)" 
     host                = "www.sanger.ac.uk
     proxy               = "http://wwwcache.sanger.ac.uk:3128"
     includeDatasets     = "" 
     martUser            = "" 
     path                = "/htgt/biomart/martservice" 
     port                = "80" 
     serverVirtualSchema = "default" 
     visible             = "1" 
   />
</MartRegistry>

On 2 Dec 2010, at 20:15, suo wrote:

Dear All,

How to put multiple databases in the registry file or make other configuration to make it happen?

In the manual, a registry file is like:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
 <MartDBLocation
        name         = "my_mart"
        displayName  = "My BioMart Database"
        databaseType = "mysql"
        host         = "localhost"
        port         = "3306"
        database     = "my_mart"
        schema       = "my_mart"
        user         = "gmod"
        password     = "gmod"
        visible      = "1"
        default      = ""
        includeDatasets = ""
        martUser     = ""
 />
</MartRegistry>

Thanks in advance!







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