3. Installing and Initializing¶
3.1. Installation Under Windows¶
Double-click on the self-extracting executable (VarSeq-Win32-2.3.0.exe or VarSeq-Win64-2.3.0.exe). It will open up an install dialog screen.
The default is to install the software in the users application data folder which is approximately:
C:\Users\<User Name>\AppData\Local\Golden Helix\VarSeq\Application\
Under Windows, you also have the option of adding a VarSeq program icon to your desktop, a Quick Launch icon, and having VarSeq available from the Start Menu.
Once VarSeq is installed, you can run the program either by using the shortcuts or by running the executable. This will launch the login and registration dialog. If you already have a VarSeq account, enter in your credentials to launch the application. Otherwise register an email address and a license key to launch the application.
3.2. Installation Under Linux Compatible Distributions¶
Download the VarSeq archive for Lin64 to a convenient user directory.
The bundle is a “.tar.gz” archive file that will extract a folder called “VarSeq”. You can extract the archive using Linux GUI or command line tools. On the command line perform the following command:
~/Programs/> tar -xzvf VarSeq-Lin64-2.3.0.tar.gz
Once extracted, you can move the resulting VarSeq folder to another location of your choice at any time.
Go into the VarSeq folder and run the VarSeq App. The program will launch and present the login and registration dialog. If you already have a VarSeq account enter in your credentials to launch the application. Otherwise, register an email address and create an account to launch the application.. You can do this with the following commands:
~/Programs/> cd "VarSeq" ~/Programs/VarSeq> ./VarSeq
Note
You may add the VarSeq folder to your path so that it can be launched from any directory. This also allows you to run scripts from various directories.
Note
You may need to install additional dependencies for VarSeq. Please see the operating system specific install guides for the most up to date details.
Please contact support if your experience issues running VarSeq on your Linux machine.
Otherwise register an email address and to create an account to launch
3.4. Installation Under Mac OS X¶
Download the VarSeq app bundle for Mac to a convenient temporary directory.
Run the installer by double clicking on the package and click and drag the VarSeq application into the Applications folder.
Go into the VarSeq folder and run the VarSeq App. The program will launch the login and registration dialog. If you already have a VarSeq account enter in your credentials to launch the application. Otherwise, register an email address and create an account to launch the application.
Note
Mac OS 10.11 or higher is required for VarSeq
3.5. Setting System Defaults with hosts.json File¶
A number of defaults for running VarSeq can be controlled by an optional hosts.json file that resides in the program folder (next to the VarSeq executable). These include a flag to limit annotation source selection to already downloaded tracks if available and a default URL for VSWarehouse.
To create a hosts.json file, you can first open VarSeq, then go to Tools > Open Folder > Program Folder. This will take you to the location of the VarSeq binary (on Mac, it will take you to the VarSeq.app/Contents folder). At this location, create a new file called hosts.json and edit it using a text editor (Note, it should not have a .txt extension). See below for example configuration options.
3.5.1. Use Only Local Sources as Latest¶
In a multi-user or clinical environment, it may make sense to not use the latest version of sources published to the public and secure annotation sources when running VarSeq or VSClinical.
Create the following hosts.json to change this behavior:
{
"localOnlyLatest": true
}
When you start VarSeq, you can see in the Help > About dialog if this flag has been set under the “Use Latest Remote Sources on Add” label.
With this flag set, the following behavior will be different:
Any opened or recently completed project will show out-of-date notifications in the upper-right for only locally downloaded annotation sources that are newer than the ones used to create the project.
Similarly, VSClinical will not show in the source version dialogs update notifications for sources that have not been downloaded.
Adding algorithms to VarSeq that have additional dependencies such as the ACMG Classifier for Variants or CNVs will select the latest local version of those dependencies if available instead of downloading the latest version from the data servers.
Note that with this flag set, you can still see and download any updated annotation source manually through the Tools > Manage Data Sources dialog by browsing the Public Annotations and Secure Annotations repositories.
It is common for all VarSeq users in a laboratory to use a shared annotations folder. Using this flag, updates can be done manually monthly or quarterly by downloading the latest version of sources like ClinVar and OMIM using this dialog. This way, all other users are not prompted to perform updates in their analysis workflows that would have implications for all other users of the shared annotations folder.
3.5.2. Change the News Feed URL¶
If your organization has a specific internal help-desk or a VarSeq support website you would like to display to users on the right-side of the welcome screen to replace the VarSeq news feed, you can customize the URL for all users.
Create the following hosts.json to change this behavior:
{
"news_feed": "http://internal-lab-domain.local/varseq-support/"
}
3.5.3. Preset the VSWarehouse URL¶
If your organization has a VSWarehouse server and multiple users, you can configure VarSeq to have the VSWarehouse URL preset for all new users.
Create the following hosts.json to change this behavior:
{
"warehouse": "http://warehouse.internal-lab-domain.local"
}
You can create a hosts.json with both of these options as well:
{
"localOnlyLatest": true,
"warehouse": "http://warehouse.internal-lab-domain.local"
}