Add to your PATH: Prodigal Infernal Aragorn Rnammer Full path to gsmm.pl (in order to run GeneMarkS)
Go here and select GeneMarkS and linux64, and download the gm_key_64: http://opal.biology.gatech.edu/GeneMark/license_download.cgi copy this "key" to your home directory: $gunzip gm_key_64.gz $cp gm_key_64 ~/.gm_key
command: chmod u+x genePrediction.sh ./genePrediction.sh -i <path_to_input_file> -o <path_to_output_file> -m <path_to_infernal_model> -h
before using: this script should run under the path where the asseblied genomes are.
prompt> perl run_gmhmm.pl list.txt
list.txt is a intermediate file which you can rename it whatever you want. It will contain a list of all the names of asseblied genomes under this path.
prompt> perl run_GeneMarkS.pl <input.fasta>
<input.fasta> should be the nucleotide sequences in fasta format.
Command: ./run_rnammer.pl <input_directory> <output_directory>
Compare to run_rnammer_new.pl, this script is more convenient to use when you don't have the name list of the files, or when you don't want to run all the files at once.
Command: ./run_rnammer_new.pl -i <test_file_list> -d <input_directory>
Command: ./run_aragorn.sh -i -o
Command: ./run_prodigal.sh <input_fasta>