The first time you start GANT, a default profile is in place so you are not required to go through the Intro Wizard. If you are presented with the Intro Wizard the first time you run GANT, then the default profile could not be initialized on your system.
The Intro Wizard allows you to quickly and easily select new data sources and modify your preferences. To start the Intro Wizard, simply choose "Options > Intro Wizard..." as pictured here:
The Intro Wizard will take you through the following 6 steps:
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Step 1: This is simply a welcome page. Click "Next" to continue with the wizard. |
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Step 2: With this screen, you will add a data source and test that it is working properly. Click "Add..." to continue. |
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If there are no options to choose from, then you need to download genomic data source plugins. See installing plugins and drivers. Select "Ensembl" from the Data Source options. Enter the values for your own local mirror of ensembl or use the default options: hostname: ensembldb.ensembl.org Click "Ok". |
Once you have chosen Ensembl as your data source, you must add two necessary drivers: ensembl and mysql. These two files should have been downloaded to the "lib" directory in your GANT installation directory and are probably named "ensj-<number>.jar" and "mysql-connector-java-<version>-bin.jar". Use the "Browse..." buttons to select the files. If you cannot locate these files, double-check your installation instructions or contact Bio::Neos for further technical support. Once you have added the two drivers, click "Test All...". If everything is setup correctly the Test column will switch from "Untested" to "Passed". |
In this step, you may add annotation data sources in the same way that you added genomic data sources in the previous step. If you do not add any annotation data sources, GANT will work but you will not see any annotation (such as domains, SNPs, secondary structures, etc.). If you'd like to add annotation data sources but no options are available, then you need to download the plugins as described in installing plugins and drivers.
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In this step, you have the option of changing annotation-specific options that affect how annotation is displayed.
If desired, select the annotation type from the drop-down box. You may change the display name (how it is displayed in the program), whether it is displayed in Full, Small, or Hidden mode by default. See Understanding Annotation for more on these modes. Once you are done, click "Next". |
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The final screen summarizes the options you have chosen as part of the Intro Wizard setup. If you are satisfied with the options, click "Finish". Otherwise, you may go back with the "Previous" button and make changes. This concludes the use of the Intro Wizard. After clicking Finish, the main GANT program will appear. To understand what to do next, you may wish to view the help documentation on Loading a Gene. |
