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| # =========================================================================== | |
| # | |
| # PUBLIC DOMAIN NOTICE | |
| # National Center for Biotechnology Information | |
| # | |
| # This software/database is a "United States Government Work" under the | |
| # terms of the United States Copyright Act. It was written as part of | |
| # the author's official duties as a United States Government employee and | |
| # thus cannot be copyrighted. This software/database is freely available | |
| # to the public for use. The National Library of Medicine and the U.S. | |
| # Government have not placed any restriction on its use or reproduction. | |
| # | |
| # Although all reasonable efforts have been taken to ensure the accuracy | |
| # and reliability of the software and data, the NLM and the U.S. | |
| # Government do not and cannot warrant the performance or results that | |
| # may be obtained by using this software or data. The NLM and the U.S. | |
| # Government disclaim all warranties, express or implied, including | |
| # warranties of performance, merchantability or fitness for any particular | |
| # purpose. | |
| # | |
| # Please cite the author in any work or product based on this material. | |
| # | |
| # =========================================================================== | |
| 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. | |
| ----------------------------------------------------------------------------- | |
| vdb-config --restore-defaults | |
| If called with this parameter the tool will bring the configuration into | |
| default state. | |
| ----------------------------------------------------------------------------- | |
| 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. | |
| ----------------------------------------------------------------------------- | |
| 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. |