There are 4 important considerations when setting up a new NextGENe user or setting up a new device with NextGENe. These include the location of reference files, the location of processing configuration files, and optionally AutoRun and User Management settings.
Multiple users on a single device and on multiple devices can share the same files and settings. And when transferring NextGENe to a new device, the same considerations are applicable.
Reference
The SoftGenetics Reference & Track Manager tool is used to manage the references and tracks that can be used by NextGENe. Use this tool by opening NextGENe -> Tools -> Reference & Track Manager.
By default, a reference imported by NextGENe is stored in C:\Users\Public\Documents\SoftGenetics\NextGENe\References. This is also the location where imported tracks (such as dbSNP, ClinVar, dbNSFP and GnomAD) are stored.
Each reference imported by NextGENe is stored in a unique folder within the ..\References\ folder. Any imported tracks are stored within the ..\References\Tracks\ folder.
The list of imported References and Tracks can be viewed in the NextGENe Reference & Track Manager tool. These folders and files can also be viewed in Windows File Explorer, as shown here.
Move or Copy the Reference and Track Files
In the case of having NextGENe transferred to a new device, be sure to use Windows File Explorer to copy these References and Tracks folders to the new device.
When the intention is to have multiple devices share the same References and Tracks, this storage path can be configured to use one of your institution's shared network drives. If a shared network drive is unavailable, then these References and Tracks folders can be copied to additional devices. It is important to note that in the case of copying the References and Tracks to multiple devices, changes to one device will not be automatically applied to other devices.
Configure the Reference & Track Manager Storage Path
A new Windows user will need to have the correct Storage Path. If the path was never updated from the default path, then the new Windows user does not need to do make any Reference updates.
In the case of References and Tracks folders being moved to new locations (on a new device or on a shared network drive), click on the NextGENe References & Track Manager's Settings button () accessible in the upper right corner, select Set Storage Path option, choose the new folder and click OK.
NextGENe Reference is now ready for the new user or device.
Processing Settings (Templates)
There are settings for pre-processing (like Format Conversion and Sequence Operations), processing (alignment and variant detection thresholds) and post-processing (like reports). Each of these settings can include dependencies, like TXT files including adapter sequences, or BED files limiting variants to specific target regions. Utilizing templates helps to keep these settings and dependencies organized.
Whether using settings or Templates, these files need to be available to new users and new devices. Follow instructions for either using Settings files of Templates.
Copy Settings to New Location
Working with Templates is a simpler approach because settings dependencies are automatically handled by NextGENe when a Template gets created, and when the Templates get moved by NextGENe to a new location. If you want to generate Templates, refer to the How to Create a Template guide for additional details.
If using settings that have not been added to templates, then copying these files to a new location may be more advanced. Because some of the settings files may include dependencies to other files (like the location of adapter sequence files and BED files), copying the settings to a new location is only the first step. Once copied to the new location, each settings file should be opened in a text editor (such as NotePad), scanned for lines that include dependencies, like a storage path to a BED file, ensure that the dependency is accessible by the new user or new device. If the dependency is not accessible by the new user or device, copy the dependency. The path within the settings file that is accessible to the new user can be updated to the new location.
Configure the Templates Storage Location
If using Templates, navigate to NextGENe -> Process -> Options to see the location where NextGENe stores Templates.
By default, Templates are stored in C:\Users\Public\Documents\SoftGenetics\NextGENe\Templates. Each Template is stored in a unique folder within the ..\Templates\ folder. If all users are sharing the same device, then this location is likely accessible by all users and Templates will be ready for use by all users.
If multiple devices are using Templates, then it is easiest to have the Templates available to all users and devices by having them stored on a shared network drive. The original device's Templates folder can easily be migrated to another location by clicking on the Set button, choosing the new folder, and clicking OK. The folders automatically get moved to the new location and paths to dependencies (like adapter sequence files and BED files) automatically get updated. Templates are now ready for this user.
IMPORTANT: Be sure to update the Template root directory for all users. If the user that is updating their Templates location includes a duplicate of a Template in the new location, then the new location's Template will be overwritten. So it may be helpful to first use Windows File Explorer to check this user's Templates folder prior to updating the Template root directory,
AutoRun
AutoRun is a tool to help automate repetitive analyses. When setting up new users and new devices, it is important to check this tool's settings to configure the location of the Job file detecting directory, as well as other settings.
AutoRun can be opened from NextGENe -> Tools -> AutoRun. Once opened, click on the Settings button to adjust settings.
IMPORANT: A single device should only have one AutoRun set to Detect for job files to be processed. If a single device has multiple AutoRun processes pointing to the same Job file detecting directory, then samples will be run in duplicate.
Once the Job file detecting directory is configured, AutoRun is ready for this new user or device.
User Management
Check the User Management settings for the user that is already configured. Settings are found in NextGENe -> Help -> User Management -> Manage Settings.
If setting up a new user on the same device, simply use the same settings as previous user.
If setting up a new device, this new device will need to be able to access the device that is hosting the SoftGenetics Server. For additional assistance, contact tech_support@softgenetics.com.