Installation
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.
Docker Compose
Docker Compose is the only supported method for installing Virtool 4.3.3.
-
Install Docker and the compose plugin on your Linux host.
-
Create a
docker-compose.yml
file to create a Virtool instance and MongoDB server.docker-compose.yml
version: "3.1" services: mongo: image: mongo:3.6 ports: - "27017:27017" volumes: - mongo:/data/db virtool: image: ghcr.io/virtool/virtool:4.3.3 environment: VT_DATA_PATH: "/data" VT_HOST: "0.0.0.0" ports: - "9950:9950" volumes: - virtool:/data volumes: mongo: null virtool: null
-
Start the services with:
docker compose -p virtool up -d
Virtool should be available on your host machine at http://localhost:9950.
Explanation
Docker is a technology that allows software to be packaged into containers.
It has many advantages over traditional software installation methods:
- Containers are portable and can be run on any system that supports Docker. This prevents issues that arise across different operating systems.
- Containers include all the software and dependencies required to run the application. In Virtool’s case this simplifies installation by removing the need to install bioinformatics tools and other dependencies.
- Upgrading the software is as simple as updating the
image
tag in thedocker-compose.yml
and runningdocker compose -p virtool up -d
.
Volumes
External Software
The Dockerized version of Virtool no longer requires installation of required bioinformatics programs. They are included in the Virtool container image.
The included software is listed for interest only.
Name | Version | Purpose |
---|---|---|
AODP | 2.5.0.1 | Motif detection |
Bowtie2 | 2.3.2 | High-throughput read alignment |
FastQC | v0.11.5 | Calculating quality metrics for sample libraries |
FLASH | 3.1b2 | Merge paired-end reads |
HMMER | 3.1b2 | Motif detection |
Skewer | 0.2.2 | Read trimming and quality control |
SPAdes | v3.8.1 | De novo assembly |