Edit EMBOSS-2.x.x/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
First comment out this line (which is used to submit batch jobs
as background processes):
boolean lforkB = aj.forkBatch(userName,passwd,environ,
embossCommand,project);
Then uncomment this line (to call runAsBatch()):
runAsBatch(aj,userName,passwd,project,embossCommand)
In the method runAsBatch() the following line will need to be changed. The batchQueue.sh is a script you will need to create to submit the emboss script (i.e. project/.scriptfile) to the batch queue system:
//EDIT batchCommand
String batchCommand = "/bin/batchQueue.sh "
+ project +
"/.scriptfile ";
The .scriptfile contains the script (environment variables
and emboss command) for the queueing system to run. This file is created
in the users area under a new project directory for that emboss
calculation. The next line:
lfork = aj.forkEmboss(userName,passwd,environ,
batchCommand,project);
should not need changing. This line calls the emboss ajax library to
submit the batch command (as that user) to the queueing software.