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:
#-----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>.*