Scripts for training of an ensemble of linear classifiers using VirFinder This pipeline is meant to be run on an HPC with a PBS scheduler.
You need to have the R package VirFinder and its dependencies installed.
please modify the
- V_DATASET = indicate here the fasta file containing viral sequences for the training set
- H_DATASET = indicate here the fasta file containing host sequences for the training set
- RESULT_DIR = indicate here the directory for the outputs
- SPLIT_SIZE = indicate the number of training example to train the models on
- ENS_SIZE= indicate the number of models to train
- KM_SIZE= indicate the kmer size to use for the training
- MAIL_USER = indicate here your arizona.edu email
- GROUP = indicate here your group affiliation
this command will submit two jobs in queue.