Specifying Preferences for the NextGENe SAD Tool
Click Preferences on the NextGENe SAD tool menu bar to open the User Preference tab. The tab displays the values that have been specified for the tool-specific directories and the number of CPU cores to use for data processing.
When the NextGENe SAD tool is installed, it is installed with default values for two of these directories and the number of cores to use for data processing. At a minimum, you must specify the Genome Reference Directory. Optionally, you can specify different values for the Workspace Directory, the Custom Model Directory, and/or the number of cores to use for processing data.
• The Workspace Directory: The directory in which all analysis results are stored. The results are stored in the analyses folder in the directory. The default value is C:\<Users>\<Users>\SAD.
 | You do not have to access the Workspace Directory to retrieve analysis results. Its location is typically for informational purposes only. You can access all analysis results from the Analysis page in the tool. See Viewing and Working with Analysis Results. |
• The Custom Model Directory: The directory in which all information for saved models is stored. The results are stored in the models folder. By default, this location is set to the same value that is specified for the Workspace Directory.
• Reference Storage Directory: SoftGenetics has created a custom genome reference to use with the tool. You download the reference from the following location:
ftp://SAD:sadtool@ftp.softgenetics.com/SAD_Build_37.zip. After you download and extract the reference genome, a folder named SAD_Build_37 is automatically created and the custom reference is stored in this folder. When you specify the Reference Storage Directory, the path must point to the directory that contains the SAD_Build_37 folder, and not to the SAD_Build_37 folder itself. You select the SAD_Build_37 folder on the Default Reference dropdown list.
ftp://SAD:sadtool@ftp.softgenetics.com/SAD_Build_37.zip. After you download and extract the reference genome, a folder named SAD_Build_37 is automatically created and the custom reference is stored in this folder. When you specify the Reference Storage Directory, the path must point to the directory that contains the SAD_Build_37 folder, and not to the SAD_Build_37 folder itself. You select the SAD_Build_37 folder on the Default Reference dropdown list.
| | If you have previously loaded reference files from a Reference directory in the Project Wizard in NextGENe, then the path to the Reference Storage Directory is set to this NextGENe Reference directory. You can store the SAD_Build_37 folder in the NextGENe Reference directory or in another directory of your choosing. |
• Use CPU Cores: The number of client cores that are dedicated to analyzing the data. The default value is one. You can increase this value, which increases tool performance and accelerates the speed of data processing; however, be aware that if other applications are running on the client at the same time as the NextGENe SAD tool, then the performance for these other applications could be impacted.
After you set the Reference Storage Directory, or after you make any changes to the Preferences default values, you must click Apply to save these preferences.