running_protect.md

Running ProTECT

ProTECT Installation

• clone the ProTECT from the repo

   git clone [email protected]:banilmohammed/protect-1.git
  

• navigate to the protect folder

   cd  protect-1
  

• create and activate the virtualenv

   virtualenv --python=python3 venv
   source venv/bin/activate
  

• install dependencies

   make prepare
  

• install bd2k extras (note this will install s3am as well but this will not used)

   make special_install
  

• install typing_extensions

   pip3 install typing-extensions
  

• install cwltool

   pip3 install cwltool==3.1.20211107152837
  

• install proper pyyaml version

   pip3 install pyyaml==5.4.1
  

• install ProTECT

   make develop
  

Running ProTECT

• create config yaml

  ProTECT --generate_config
  

• update the config file with the file paths to the sample data files and the file paths to where the human genome reference will be downloaded

• create working dir before the run

• run ProTECT

  ProTECT --config path/to/config_file.yaml --workDir path/to/workDir/ path/to/jobStore --disableCaching --cleanWorkDir never --reference
  

• the reference flag downloads the human genome reference to /mnt/neoepitopes/protect_references/, if not specified human genome reference files will not be downloaded, and ProTECT will be run as normal

• by default --reference will download references to /mnt/neoepitopes/protect_references