Depreciated

SGE

First, load the module maker. Then follow the steps:
*Create your maker control files:

 maker -CTL

*Edit you control files. For example, my test files look like this:

maker_exe.ctl

 #-----Location of Executables Used by Maker/Evaluator  
 formatdb:/mnt/home/module/apps/biology/blast/2.2.22/bin/formatdb #location of  NCBI formatdb executable  
 blastall:/mnt/home/module/apps/biology/blast/2.2.22/bin/blastall #location of NCBI blastall executable  
 xdformat: #location of WUBLAST xdformat executable  
 blastn: #location of WUBLAST blastn executable  
 blastx: #location of WUBLAST blastx executable  
 tblastx: #location of WUBLAST tblastx executable  
 RepeatMasker:/mnt/home/module/apps/biology/repeatmasker/3.2.8/bin/RepeatMasker #location of RepeatMasker executable  
 exonerate:/mnt/home/module/apps/biology/exonerate/2.2.0/bin/exonerate #location of exonerate executable  
 ...  
'''maker_opts.ctl'''  
 #-----Genome (Required for De-Novo Annotation)  
 genome:dpp_contig.fasta #genome sequence file in fasta format  
 ...

maker_bopts.ctl

#-----BLAST and Exonerate Statistics Thresholds  
 blast_type:ncbi #set to 'wublast' or 'ncbi'

Now your ready to maker.

*If you want to use the regular version of maker, create an sge script for submission:

#!/bin/sh  
 #$ -cwd  
 #$ -N maker-test  
 #$ -V

 . /usr/modules/init/bash  
 module load maker

 maker maker_exe.ctl maker_opts.ctl maker_bopts.ctl

*If you want to use the mpich2 version of maker, create a different sge submission script:
mpitest.sge

 #!/bin/sh  
 #$ -cwd  
 #$ -N makermpi  
 #$ -pe mpich2_smpd 5  
 #$ -V  
 #$ -e makermpi.e  
 #$ -o makermpi.o

 . /usr/modules/init/bash  
 module load mpich2 maker

 port=$((JOB_ID % 5000 + 20000))  
 mpiexec -n 10 -machinefile $TMPDIR/machines -p $port mpi_maker maker_exe.ctl maker_opts.ctl maker_bopts.ctl -f

*Then submit to sge and your done:

qsub <name of your submission file>

*Check the output of your job by running:

tail -f <name of your job>.*