What is Blast2Go 

Blast2go is a software tool for the automated, high-throughput functional annotation of novel sequence. Blast2go use BLAST to identify similar sequences and then transfers existing functional annotation from hits to query sequences.

Requirements

Webstart file from HERE 

JAVA enabled machine 

How to run Blast2go on Ubuntu

Although Ubuntu come with its own java version but I found that it didn't work for Blast2go. Therefore I decide to install Oracle Java (JDK). You can install Oracle Java (JDK) by these commands one by one

sudo add-apt-repository ppa:webupd8team/java

sudo apt-get update

sudo apt-get install oracle-java8-installer

You can your java version by this command

java -version

it should print like this in terminal

java version "1.7.0_67"
Java(TM) SE Runtime Environment (build 1.7.0_67-b01)
Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)

Note to me

Above command will install  Oracle Java 8 but I found that Blast2go didn't work for Oracle
 Java 8 therefore I decide to install previous  version of Oracle Java. You can replace 8 with 
6 or 7 to install Oracle Java 6 or Oracle Java 7 

Now we are all set. Just go to your working directory and type

javaws blast2go1000.jnlp

Remember that I downloaded the 1000MB version of Blast2go therefore my command include the '1000'. It should as per your requirement.