05. Toolkit Configuration
If you are using SRA Toolkit version 2.4 or higher, you should run the configuration tool, located within the bin subdirectory of the Toolkit package.
Go to the "bin" subdirectory for the Toolkit and run the following command line:
./vdb-config -i
A window will open and present the below screen.
The tool has 7 pages for different aspects of settings.
The top line of buttons is visible on all 7 pages.
You use the buttons by pressing the letter highlighted in red, or by pressing tab-key until the wanted button is reached and then pressing the space- or the enter-key.
[save] ... save the current settings, but do not exit
[exit] ... exit the tool, asking to save if settings have been changed
[verify] ... not yet implemented
[discard] ... discard all changes made ( since start or last save )
[default] ... set values to default
The first page: MAIN, contains just these 2 settings.
[Enable Remote Access] ... if enabled, instructs the sra-tools to fetch data from remote locations via https.
Remote locations are either servers at NCBI, AWS or GCP. If you turn this checkbox off and you have no local data available ( via download ), the sra-tools cannot find any data.
[Use Site Installation] ... this setting is only visible if you admin has configured a local site-repository.
This page controlls the caching behavior.
In order for your commands to complete successfully, the toolkit needs sufficient free space. Genomics datasets are quite large; you may need 100's of GB of free space. This is the primary concern when choosing the Workspace Location. Do you have enough free space there for what you intend to do?
If you need to change the Workspace Location, use the tab key to move the cursor (shown red here) to the change button and press space or enter.
This will bring up the file navigation dialog (see below).
if you already know the path to the directory, you may use the Goto button to directly enter that path. Once you have entered or navigated to the correct directory, press tab to get to the OK button to return to the previous screen.
Once you are happy with the settings, use the tab key to get to the Save button and press enter or space.
Press enter or space one more time, then tab to the Exit button and press enter or space. You will then be returned to your shell command prompt.