We recommend the following minimum specifications for running a Virtool server:
Higher CPU clock speeds and core counts will allow more operations to be run in parallel.
Virtool works best in modern browsers including Chrome, Firefox, Safari, and Edge. Internet Explorer is not supported.
Download the latest Virtool release from the Virtool website and unpack the downloaded archive.
tar -xvf virtool.tar.gz
Move the unpacked directory to your installation location:
mv virtool /opt
Start Virtool by executing the
Virtool can be configured to run as a service on your Linux host using
systemd. These instructions make the following assumptions:
Create a new service unit file for Virtool at
[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
sudo systemctl daemon-reload
The service configuration ensures that Virtool doesn’t start until
mongod and networking services have started.
systemdunit files. See Creating and Modifying systemd Unit Files.
To start Virtool using
systemd, issue the following command:
sudo systemctl start virtoold.service
You can check if Virtool is running with the following command:
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
The service can be stopped using the following command:
sudo systemctl stop virtoold.service
You can check if the Virtool service has stopped using the
sudo systemctl status virtoold.service
The provided service file allows Virtool to be run on system start.
virtoold.service to make it start when the system is initializing:
sudo systemctl enable virtoold.service
This can be undone by disabling the service:
sudo systemctl disable virtoold.service
Virtool uses MongoDB v3.6.0+ as a database service. You will have to get MongoDB running before starting Virtool. We highly recommend installing and updating MongoDB through your Linux package manager.
The MongoDB documentation provides step-by-step instructions for installing MongoDB on common Linux distributions:
Once you have installed MongoDB, ensure it is running by issuing the following command:
sudo systemctl status mongod.service
You will receive an output similar to the following if MongoDB is running:
● mongod.service - High-performance, schema-free document-oriented database Loaded: loaded (/etc/systemd/system/mongod.service; disabled; vendor preset: enabled) Active: active (running) since Fri 2017-04-21 15:55:59 PDT; 2s ago Main PID: 11844 (mongod) Tasks: 14 Memory: 31.1M CPU: 95ms CGroup: /system.slice/mongod.service └─11844 /usr/bin/mongod --quiet --config /etc/mongod.conf
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.
|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|