Instructions to Setup Connection to Spormann Geneious Database

For the cost of a burrito a friend of the Spormann Lab and Hopkins TA veteran Steve Biller helped setup a Geneious database on our file server, based on the MySQL platform. It is meant to be a means for sharing adn storing Geneious files that are of relevance to the rest of the lab, especially those that are related to the strain database.  For the time being there is no quota on the size of the database, and everyone will have access to every file/directory.  Everything on this database will be backed-up with the same protocol and high-redundancy as the User Shares on SP-FS. Interaction with the database is very easy and built into Geneious.

SETUP
 

  1. Open Geneious  ( if you don't already have it, download it at:   http://www.geneious.com/ and install it)
  2. Click on 'Server Databases'
  3. Click on 'Connect to a database'
    Username: laball
    Password: alfred
  4. Host URL: sp-fs.stanford.edu
  5. Check the box labeled 'Custom'
  6. Enter Port: 3306
  7. Database Name: spostrains
  8. Database Vendor: MySQL
    make sure 'Connect account' is checked
  9. Download the driver .jar file (attached, bottom). Save it in an out-of-the-way, stable location on your system.
  10. Click on 'More Options'
    Driver .jar file:
        -- click 'Browse' and locate the file on your system labeled
        "mysql-connector-java-3.1.14-bin.jar"
    click 'enter'
  11. Make sure 'Custom class name & URL prefix is unchecked

    From inside Geneious the screen should look like:

    Geneious DB screen shot

     

  12. Click 'OK' (done with setup)

Usage

Once this is set up, find your folder in the Spostrains directory. If it is not there feel free to add it by clicking the '+' button for adding new folders. You add files by dragging and dropping just like in Mac's Finder or Windows' Explorer.  For large files (or large numbers of files) be patient, it might take some time to transfer them. They are literally being moved from your computer onto the server. Once they are on the server, you can alter the file as-is using Geneious as you always would, and the file never has to leave the server.  You will also be able to do this from anywhere in the world, provided your connection is fast enough and you have 'VPN'-ed into the Clark Center network.

AttachmentSize
mysql-connector-java-3.1.14-bin.jar448.33 KB
0 March 23, 2009