From Array Suite Wiki
This option allows ArrayServer administrators to specify a command that will be executed at startup, on the linux EC2 instance, before any job is started.
The command needs to be specified in ArrayServer.cfg, and will be executed for all jobs running in the cloud, on the EC2 instances.
The following command, specified in the Cloud section of ArrayServer.cfg, will copy test.txt file from one S3 bucket to another.
[Cloud] ... CustomCommand=aws s3 cp s3://east.test.omicsoft/SGECloudFolder/test.txt s3://east.geneticsland.omicsoft/Samples/test.txt