2.1.1 vAMPirus startup script
A startup script written in BASH is provided within the vAMPirus installation directory that will automatically install dependencies and prepare the vampirus.config file for use. Users can deploy this script to download the Nextflow workflow manager and Conda package management system if these programs are not already installed/accessible on the computer system. The script can also be directed to download one or more protein/taxonomy databases to be used in vAMPirus taxonomy processes. Available databases include: 1. The proteic version of the Reference Virus DataBase (RVDB, Bigot et al., 2020), 2. NCBI virus protein RefSeq database (Brister et al., 2015), and 3. Complete NCBI NR protein database (O’Leary et al., 2016). If directed to do so, the startup script will also download the NCBI Taxonomy Database (Schoch et al., 2020) and last common ancestor (LCA) information for sequences curated within the RVDB (Bigot et al., 2020). The script then edits the vAMPirus configuration file with the updated paths to any downloaded databases and to the vAMPirus installation directory. Lastly, text documents that include general next steps for the user and commands to test the installation are printed in the vAMPirus directory. If test analyses complete successfully, the user then updates the configuration file with project-specific parameters (e.g., project name, database for taxonomy inference, primer sequence information, number of allocated threads, working memory, scheduling manager) prior to running vAMPirus on a dataset.