VarSeq System Requirements

Supported Operating Systems

Golden Helix VarSeq and SVS are cross-platform natively compiled applications.

The following operating systems are supported:

  • 64-bit Windows 10, 11, 2019 Server, 2022 Server
  • Ubuntu Linux 20.04, 22.04 or 24.04 (64-bit only)
  • Enterprise Linux 7, 8 or 9 (RHEL, CentOS or Rocky) (64-bit only)
  • Mac OS X 10.13 or later

Minimum Hardware Requirements (Per User)

  • 6GB of RAM
  • Multicore CPU
  • 100GB of space available for annotations and projects

The VarSeq Suite is very resource efficient, but analyzing large genomic data sets requires RAM and CPU resources proportionate to the type of data processed. As the NGS data set scales to exomes and genomes, more RAM is required and it is suggested that more CPU cores are added to perform the analysis.

The following recommended configurations are sized to support different sized workflows.

Small Workflow Hardware Recommendations (Per User)

Small workflows are include single or multi-sample gene panel analysis (up to hundreds of genes) for a single VarSeq user.

  • 8GB of RAM
  • 4+ CPU cores
  • 100GB of space available for annotations and projects

Medium Workflow Hardware Recommendations (Per User)

Medium workflows include single or multi-sample exome analysis (thousands of genes) for a single VarSeq user.

  • 16GB+ of RAM for single users or 32GB for servers
  • 8+ CPU Cores
  • 1TB of space available for annotations and projects

Large Workflow Hardware Recommendations (Per User)

In general, large workflows are considered to be many-sample whole genome analysis for a single VarSeq user. This also includes cohort analysis of thousands of samples (VarSeq is regularly tested up to 250,000 samples) in a single project, regardless of the number of variants.

  • 32GB+ of RAM
  • 12+ CPU Cores
  • 1TB of space available for annotations and projects

Warehouse Server Configurations

VSWarehouse requires a Linux server running Ubuntu 20.04, Ubuntu 22.04 or RHEL/CentOS 7.

A VSWarehouse server should generally be configured with a Medium or Large Workflow configuration depending on the type of data regularly added to the VSWarehouse. Large cohort projects that get regularly updated should be configured with 64GB of RAM.

Deployment Considerations

You may consider the following when planning your VarSeq deployment

Multi-User Server Configurations

You can install your Golden Helix software solution on a server with multi-user access and shared resources. Individual users should each have a separate operating system login to the server, so they have a dedicated session and personalized experience. Each user will also take up a single license seat, just as if they were using their own dedicated hardware.

The server hardware requirements should be planned to support have CPU and RAM based on the workflow type listed above per concurrent user. For example, if you expect you may have three active users on a server doing exome analysis, we suggest the server have 48GB of RAM and 24 cores.

For Windows, the Windows Server is required with an appropriate configuration and Microsoft licenses to support Remote Desktop for all uses. We support Windows Server 2019.

On Linux, clients can log in from any operating system using SSH and open the Golden Helix software using X11-tunneling to interact with the software. On windows, we suggest a solution like MobaXterm that provides a all-in-one SSH client and X11 server to enable easy logging in, file transfer and opening of remote GUI applications.

Proxy Settings, Firewalls and AntiVirus

To license the software and access public data resources, Golden Helix VarSeq and SVS must be able to access the internet. Limited support for “air-gapped” and offline installations is supported. Please contact our support team for details

Golden Helix VarSeq and SVS can be configured to access the internet through a SOCKS5 or HTTP/HTTPS Tunneling Proxy. Go to Tools -> Proxy Settings… to configure.

The software only needs to make outgoing connections on standard HTTP/HTTPS ports and protocols. If a local firewall is installed that prevents these types of outgoing connections (this is very uncommon), firewall rules will need to be created to whitelist the software.

Note we have run into numerous issues where aggressive anti-virus programs prevent the product from performing normal operations such as opening files and logging in. You may need to whitelist Golden Helix executables or disable these tools to perform your analytics.

Whitelisting GHI websites

If your institution needs to whitelist Golden Helix servers at the firewall or internet gateway level at an institution level, the below table lists the servers, ports and IP addesses for whitelisting: 

Server / Location Ports IP Address for Whitelisting (US) 80, 443 (http, https) (EU) 80, 443 (http, https) (AU/Asia) 80, 443 (http, https) (IN)80, 443 (http, https) 443 (https) 
Updated on April 25, 2024

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