GETTING_STARTED.txt

Hello there, to get started with vAMPirus you can run any of the following depending on your situation:

Before running anything, you can learn a little about the vampirus_startup.sh with the help info:

        bash vampirus_startup.sh -h

You will see ->

General execution:

vampirus_startup.sh -h [-d 1|2|3|4] [-s]

    Command line options:

        [ -h ]                       	Print help information

        [ -d 1|2|3|4 ]                Set this option to create a database directiory within the current working directory and download the following databases for taxonomy assignment:

                                                    1 - Download the proteic version of the Reference Viral DataBase (See the paper for more information on this database: https://f1000research.com/articles/8-530)
                                                    2 - Download only NCBIs Viral protein RefSeq database
                                                    3 - Download only the complete NCBI NR protein database
                                                    4 - Download all three databases

        [ -s ]                       Set this option to skip conda installation (you can use if you plan to run with Singularity and the vAMPirus Docker container)


1. Run vampirus_startup.sh to install Miniconda3 and and install Nextflow:

        bash vampirus_startup.sh

2. Run vampirus_startup.sh to install Miniconda3, download the RVDB database and install Nextflow:

        bash vampirus_startup.sh -d 1

3. Run vampirus_startup.sh to install Nextflow and the RVDB database (this would be the command if not using conda or you already have conda installed/environment built):

        bash vampirus_startup.sh -s -d 1