adapted the augustus script used for gene prediction for A.D.Armitage's PhD thesis for use using the SGE and the emr directory structure.
corrected syntax error
Added submit_augustus.sh script to submit augustus_pipe.sh jobs to the SGE and predict the proteome for all the isolates in the data structure.
Corrected order of copying infiles. Renamed temporary directory.
Augustus pipe now working.
Untested pipe to train maker to perform gene prediction.
Added script to train augustus parameters to find gene models from supplied EST evidence or supplied gene models.
Merge branch 'augustus'