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VirFinder_parrallel_eval

Pipeline for VirFinder use on dataset. Parallelized for HPC use.

The complete pipeline will run VirFinder on all submitted files.

Requirements

VirFinder

VirFinder is an R package available at https://github.com/jessieren/VirFinder

Quick start

Edit scripts/config.sh file

please modify the following attributes

  • DATASET_DIR: path to the directory where the data is store

  • MOD : path to VirFinder model to use. If set to "default", the built-in VirFinder model will be used

  • RESULT_DIR : path to the output directory

  • OUTNAME : indicate here the name to use for the output files

  • MAIL_USER : indicate here your arizona.edu email

  • GROUP : indicate here your group affiliation

You can also modify

  • BIN = change for your own bin directory.
  • MAIL_TYPE = change the mail type option. By default set to "bea".
  • QUEUE = change the submission queue. By default set to "standard".

Run pipeline

Run

./run.sh

This command will place one job in queue.