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# National Center for Biotechnology Information

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The tool 'vdb-config' can be used to inspect or change the configuration

of the sra-toolkit.

When called without any parameters the tool reports the current configuration

in xml-format. No changes are made.

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vdb-config --restore-defaults

If called with this parameter the tool will bring the configuration into

default state.

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vdb-config -i

This will present the user with a colored configuration dialog.

The tab-key and the cursor-keys navigate the dialog. The item with the little

red square has the focus. A button or a checkbox can be 'pressed' with the

space or enter-key. To get out of the dialog without saving any changes

press the '6'-key or the 'q'-key or navigate to the 'exit'-button at the

bottom of the dialog and press the space or enter-key.

The "data source" part:

The "NCBI SRA" labeled checkbox enables/disables remote access to the SRA-

accession stored at NCBI. As long as the computer has internet-access and this

checkbox is enabled the user can access SRA-accessions directly without

downloading them.

A command like 'sra-pileup SRR341578' at the command-line will produce pileup

output of the given accession even if this accession has not been downloaded

before.

The tool will download the data on the fly from our servers.

There might be a checkbox labeled "site" below the "NCBI-SRA" one. If this

checkbox is not available you do not have a 'site'-installation of SRA-data.

If it is visible you do have such a site-installation and you can disable

access to this data.

The "local workspaces" part:

At the top are 2 buttons "import dbGaP-project" and "set default import path".

If you are not using dbGaP-projects (The database of Genotypes and Phenotypes)

you can ignore these 2 buttons.

The "import dbGaP-project" button presents you with another dialog to select

a ngc-file. You can navigate the directories of your computer to find and

select one of these files. By default the focus is in the files-list. It may

be empty.

Use the cursor-key: 'up' to focus the 'directories'-list. If you press enter

on any of the listed directory-names you change into this directory.

The '[ .. ]' entry brings you back into the parent directory. If you see

ngc-files in the lower 'files'-list press the tab-key to switch to the

'files'-list. Press enter on one of them to select this file for import. You

will see a success-message if the import was performed without errors.

On Windows you cannot switch from one drive-letter

to another when selecting.

The "set default import path" gives you the opportunity to specify a different

default location for dbGaP-projects - for instance if your home directory is

not big enough. You can always change the location for your dbGaP-project

after the import.

Below the 2 buttons is a list of local repositories. If there are no

dbGaP-projects this list has only one entry "Open Access Data". This is the

location where accessions get downloaded and cached. You can change these

locations if for instance your home directory where they are created by

default does not have enough space.

The change button brings up a directory-select dialog.

If you made any changes like enabling/disabling or changed a location, the

change is only written to the configuration if you exit the dialog via the

'save and exit' button.

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vdb-config -i --interactive-mode textual

This will present the user with a purely textual and sequential dialog. It is

intended to be used if the colored mode does not work, maybe because of

console issues.