Running HPVDetector in command line mode:
HPVDetector can be executed from command line of Linux/Unix systems. Edit the config.txt file in root directory of HPVDetector to make changes of the variables/path required for the tool. There should be no changes made other than following:
1.mode should be specified as “Integration” or “QuickDetect”
Ex.: mode=QuickDetect
2.bwa should be specified as path to the BWA 0.6.2 executable
Ex.: bwa=/home/bwa-0.6.2/bwa
3.picard should be specified as path to the Picard tool 1.100 directory
Ex.: picard=/home/HPVDetector_v1.0/picard-tools-1.100/
4.hpv_bwa_index should be specified as path to HPV_index_files supplied with the tool
Ex.: hpv_bwa_index=/home/ HPVDetector_v1.0/HPV_index_files/HPV_143types_EBVref
5.hpv_human_bwa_index should be specified as path to Human_HPV_index_files supplied with the tool
Ex.: hpv_human_bwa_index=/home/HPVDetector_v1.0/Human_HPV_index_files/human_HPV
6.annotation_dir should be specified as path to annotation_files supplied with the tool
Ex.: annotation_dir=/home/HPVDetector_v1.0/annotation_files/
7.threads should be specified as whole number (should not exceed the actual number of threads available in the system)
Ex.: threads=4
8.After making above changes, execute HPVDetector as:
./HPVDetector config.txt