1# =========================================================================== 2# 3# PUBLIC DOMAIN NOTICE 4# National Center for Biotechnology Information 5# 6# This software/database is a "United States Government Work" under the 7# terms of the United States Copyright Act. It was written as part of 8# the author's official duties as a United States Government employee and 9# thus cannot be copyrighted. This software/database is freely available 10# to the public for use. The National Library of Medicine and the U.S. 11# Government have not placed any restriction on its use or reproduction. 12# 13# Although all reasonable efforts have been taken to ensure the accuracy 14# and reliability of the software and data, the NLM and the U.S. 15# Government do not and cannot warrant the performance or results that 16# may be obtained by using this software or data. The NLM and the U.S. 17# Government disclaim all warranties, express or implied, including 18# warranties of performance, merchantability or fitness for any particular 19# purpose. 20# 21# Please cite the author in any work or product based on this material. 22# 23# =========================================================================== 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