Installation Updated September 1, 2020

System Requirements

We recommend the following minimum specifications for running a Virtool server:

  • Linux operating system
  • 32 GB RAM
  • 1 TB fast storage
  • 1 Gb network connection

Higher CPU clock speeds and core counts will allow more operations to be run in parallel.

Browsers

Virtool works best in modern browsers including Chrome, Firefox, Safari, and Edge. Internet Explorer is not supported.

Install the Server

  1. Download the latest Virtool release from the Virtool website and unpack the downloaded archive

    tar -xvf virtool.tar.gz
    
  2. Move the unpacked directory to your installation location

    mv virtool /opt
    
  3. Start Virtool by executing the run file

    ./run
    

Run as a Service

Virtool can be configured to run as a service on your Linux host using systemd. These instructions make the following assumptions:

  • You run Virtool using a dedicated user called virtool.
  • Virtool is installed at /home/virtool/app.
  1. Create a new service unit file for Virtool at /etc/systemd/system/virtoold.service

    This service configuration ensures that Virtool doesn’t start until mongod and networking services have started.

    virtoold.service

    [Unit]
    Description=A application server for NGS-based virus diagnostics.
    Documentation=https://www.virtool.ca/docs
    Requires=mongod.service network.target
    After=mongod.service network.target
    
    [Service]
    Type=simple
    User=virtool
    WorkingDirectory=/home/virtool/app
    ExecStart=/home/virtool/app/run
    
    [Install]
    WantedBy=mongod.service network.target mnt-array0.mount
    
  2. Reload the systemd configuration

    sudo systemctl daemon-reload
    

Start the Service

The new Virtool service can be started using systemd.

  1. Issue the following command:

    sudo systemctl start virtoold.service
    
  2. Check if Virtool is running

    sudo systemctl status virtoold.service
    

    The service status should look something like this if Virtool is running:

    ● virtoold.service - A application server for NGS-based virus diagnostics.
      Loaded: loaded (/etc/systemd/system/virtoold.service; enabled; vendor preset: enabled)
      Active: active (running) since Fri 2020-01-31 09:11:50 PST; 1h 6min ago
        Docs: https://www.virtool.ca/docs
    Main PID: 1523 (run)
        Tasks: 203 (limit: 7372)
      CGroup: /system.slice/virtoold.service
              ├─ 1523 /home/virtool/app/run
              ├─29957 /home/virtool/app/run
              ├─30106 python /usr/local/bin/spades.py -t 14 -m 60 -s /mnt/array0/virtool/data/samples/uaofeeaw/analysis/nqy9xo0n/unmapped_hosts.fq -o /tmp/tmplojfnvz9 -k 21,33,55,75
              ├─32037 /home/virtool/app/run
              └─32194 /opt/spades/bin/spades /tmp/tmplojfnvz9/K21/configs/config.info
    
    

Stop the Service

The Virtool service can be stopped using systemd.

  1. Issue the following command:

    sudo systemctl stop virtoold.service
    
  2. Check that the Virtool service has stopped using the status subcommand

    sudo systemctl status virtoold.service
    

Run on System Start

The service file provided above allows Virtool to be started automatically on system start.

  1. Enable the virtoold.service to make it start when the system is initializing

    sudo systemctl enable virtoold.service
    
  2. This can be undone by disabling the service

    sudo systemctl disable virtoold.service
    

External Software

Virtool relies on a number of common bioinformatics programs. These should be available in your PATH so Virtool can find them. You will encounter errors if these programs are not available.

Name Version Purpose
Skewer 0.2.2 Read trimming and quality control
FastQC v0.11.5 Calculating quality metrics for sample libraries
Bowtie2 2.3.2 High-throughput read alignment
SPAdes v3.8.1 De novo assembly
HMMER 3.1b2 Motif detection
FLASH 3.1b2 Motif detection
AODP 2.5.0.1 Motif detection