Blastz

Blastz is installed on the SP. It should appear on your default path as
blastz.  The only documentation provided with blastz appears to be a
README.pdf file that is installed in /miscapps/blastz/doc.  

The simplest way to run it as a loadleveler job is to use the serialjob
script.

	serialjob blastz options_to_blastz 

will submit a job to the class a serial queue that can run for 48 hours.
To submit to the class b serial queue which allows jobs to run for 30
days,

	serialjob blastz options_to_blastz -- -class b




clustalx

Clustalx is ready on both the SP and on solar.  It should be on your
default path on both machines. (Installed in /miscapps/clustalx with
sym link from /usr/local/bin.) To run it
just type 

	clustalx

To use the interactive queue on solar for runs that will use more than 20 
minutes of processor time, type

	qsub -I 

and press return.  You'll see the message of the day scroll by again.
Now, run clustalx.

When you're finished running clustalx, be sure to exit from the current
shell to release resources back to the system. Just type

        exit

and press return.




Meme

The parallel version of meme is on the SP and ready for you to test.
The script for submitting meme jobs is /miscapps/batch/bin/memejob.
memejob's command-line options are identical to those of the original meme
script.  If you use the -p option a parallel job will be submitted.  The
parameter specified with -p is the number of nodes.  Four processors
will be used on each node, so -p 4 means 16 processors.  If -p is not
used a serial job is submitted.  If you are unfamiliar with the command
line options, run memejob with no options to obtain usage information. 

MEME jobs create two files in the directory that is your current
working directroy when you run the script.  They will be named
memeXxY.output.Z and meme.XxY.error.Z, where X is the number of
nodes used, Y is the number of processors per node and Z is the job
number. The output file contains output from meme, and the error
file contains whatever messages meme sends to the standard error.