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24
25
26The tool 'vdb-config' can be used to inspect or change the configuration
27of the sra-toolkit.
28
29When called without any parameters the tool reports the current configuration
30in xml-format. No changes are made.
31
32-----------------------------------------------------------------------------
33
34vdb-config --restore-defaults
35
36If called with this parameter the tool will bring the configuration into
37default state.
38
39-----------------------------------------------------------------------------
40
41vdb-config -i
42
43This will present the user with a colored configuration dialog.
44
45The tab-key and the cursor-keys navigate the dialog. The item with the little
46red square has the focus. A button or a checkbox can be 'pressed' with the
47space or enter-key. To get out of the dialog without saving any changes
48press the '6'-key or the 'q'-key or navigate to the 'exit'-button at the
49bottom of the dialog and press the space or enter-key.
50
51
52The "data source" part:
53
54The "NCBI SRA" labeled checkbox enables/disables remote access to the SRA-
55accession stored at NCBI. As long as the computer has internet-access and this
56checkbox is enabled the user can access SRA-accessions directly without
57downloading them.
58
59A command like 'sra-pileup SRR341578' at the command-line will produce pileup
60output of the given accession even if this accession has not been downloaded
61before.
62The tool will download the data on the fly from our servers.
63
64
65There might be a checkbox labeled "site" below the "NCBI-SRA" one. If this
66checkbox is not available you do not have a 'site'-installation of SRA-data.
67If it is visible you do have such a site-installation and you can disable
68access to this data.
69
70
71The "local workspaces" part:
72
73At the top are 2 buttons "import dbGaP-project" and "set default import path".
74
75If you are not using dbGaP-projects (The database of Genotypes and Phenotypes)
76you can ignore these 2 buttons.
77
78The "import dbGaP-project" button presents you with another dialog to select
79a ngc-file. You can navigate the directories of your computer to find and
80select one of these files. By default the focus is in the files-list. It may
81be empty.
82Use the cursor-key: 'up' to focus the 'directories'-list. If you press enter
83on any of the listed directory-names you change into this directory.
84The '[ .. ]' entry brings you back into the parent directory. If you see
85ngc-files in the lower 'files'-list press the tab-key to switch to the
86'files'-list. Press enter on one of them to select this file for import. You
87will see a success-message if the import was performed without errors.
88On Windows you cannot switch from one drive-letter
89to another when selecting.
90
91The "set default import path" gives you the opportunity to specify a different
92default location for dbGaP-projects - for instance if your home directory is
93not big enough. You can always change the location for your dbGaP-project
94after the import.
95
96
97Below the 2 buttons is a list of local repositories. If there are no
98dbGaP-projects this list has only one entry "Open Access Data". This is the
99location where accessions get downloaded and cached. You can change these
100locations if for instance your home directory where they are created by
101default does not have enough space.
102The change button brings up a directory-select dialog.
103
104If you made any changes like enabling/disabling or changed a location, the
105change is only written to the configuration if you exit the dialog via the
106'save and exit' button.
107
108-----------------------------------------------------------------------------
109
110
111vdb-config -i --interactive-mode textual
112
113This will present the user with a purely textual and sequential dialog. It is
114intended to be used if the colored mode does not work, maybe because of
115console issues.
116