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 is the only supported method for installing Virtool 4.3.3.
docker-compose.ymlfile to create a Virtool instance and MongoDB server.
version: "3.1" services: mongo: image: mongo:3.6 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.
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
imagetag in the
docker compose -p virtool up -d.
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.
|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|
|Skewer||0.2.2||Read trimming and quality control|
|SPAdes||v3.8.1||De novo assembly|