Some additional options must be set to run shotmap on a remote, SGE configured distributed computing cluster (invoked using --remote):
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You must set up passphrase-less SSH to your computational cluster. In this example, the cluster should have a name like "compute.cluster.university.edu". Follow the links at "https://www.google.com/search?q=passphraseless+ssh" in order to find some solutions for setting this up.
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Cluster configuration file: you will need point shotmap to a file that contains a SGE submission script configuration header by using the --cluster-config option. A cluster configuration file essentially contains the header information that you would include in a SGE or PBS submission script that is run on your high performance computing cluster. These configurations are often system specific; you may need to consult with the system administrator. See here for an example.
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Ensure that gene prediction and search algorithms being invoked by shotmap are installed and accessible via the $PATH environmental variable on the remote machine.
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Remote options: Invoke and properly set the following remote options (see below for details): --remote, --rhost, --rdir, --stage
Note that --stage need not be invoked everytime you run shotmap on your remote cluster.