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.