Prodigal
Prodigal is a program to perform fast, reliable protein-coding gene prediction for prokaryotic genomes.
Version 2.6.3 is installed on the CSF. It has been compiled with the gcc compilers.
Restrictions on use
There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v3 license and all usage should adhere to that license.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
Load one of the following modulefiles:
module load apps/gcc/prodigal/2.6.3
Running the application
Please do not run prodigal on the login node. Jobs should be submitted to the compute nodes via batch. You may run on the login node:
prodigal -h
to see a list of command-line flags accepted by the application.
Serial batch job submission
Prodigal is a serial application only. Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory # We now load the modulefile in the jobscript module load apps/gcc/prodigal/2.6.3 prodigal arg1 arg2 ...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.