ScatterServer.pl -p <blast_executable_name> -d /DB_DIR/<database_name> <OPTIONS>

Command Line Options

• SCATTER Options
  
  --scatterclient <filename>
  
  Lets you input the name of the SCATTER client file. The default is ScatterClient.pl
  
  --querylist <filename>
  
  Lets you input the name of the querylist file containing the list of query names. In the event that the querylist file is not supplied, SCATTER assumes that the individual query files are present in the $SCATTER_HOME/seq/ directory and are named query1, query2, …
  
  --timer
  
  This option allows you to time the total execution time.
  
  --verbose
  
  This option will print out the progress of the run, including the setting up and shutting down of the clients and servers.
  
  --splitfile <filename>
  
  This option allows one to input a file containing multiple queries in fasta format. The file split.pl provided along with the package will split this file into different queries and put them in the $SCATTER_HOME/seq directory.
  
  --port <port number>
  
  This option allows the user to specify a server port. If not specified, a random port number will be generated and used as the server port.
  
  --numclients <number>
  
  This option allows the user to set the number of clients to be generated per node. Make sure that the number is always less than or equal to the number of processors per node.
  
  --version
  
  This option used along with the ScatterServer.pl command prints the current version of SCATTER.
  
  --scheduler <option>
  
  This option allows you to specify a scheduler. The two types of scheduler currently available are self and chunking. The default is self. Currently, since the query directory is NFS mounted, there doesn't seem to be too much of an advantage to be gained in carrying out chunking. In fact it might even make things slower. However, future versions might not use NFS mounted directories.
  
  --chunksize <integer>
  
  This option sets the chunksize when used along with the chunking scheduler.



• BLAST Options
  
  The only difference here is that all the Upper Case options for blastall have now been changed to a double letter. For e.g., blastall option "-A" has been changed to "-AA". All other options are the same as those for BLAST.