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annotate libs/sratoolkit.2.8.0-centos_linux64/README-vdb-config @ 3:38ad1130d077 draft

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author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 # ===========================================================================
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2 #
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3 # PUBLIC DOMAIN NOTICE
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4 # National Center for Biotechnology Information
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5 #
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6 # This software/database is a "United States Government Work" under the
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7 # terms of the United States Copyright Act. It was written as part of
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8 # the author's official duties as a United States Government employee and
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9 # thus cannot be copyrighted. This software/database is freely available
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10 # to the public for use. The National Library of Medicine and the U.S.
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11 # Government have not placed any restriction on its use or reproduction.
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12 #
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13 # Although all reasonable efforts have been taken to ensure the accuracy
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14 # and reliability of the software and data, the NLM and the U.S.
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15 # Government do not and cannot warrant the performance or results that
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16 # may be obtained by using this software or data. The NLM and the U.S.
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17 # Government disclaim all warranties, express or implied, including
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18 # warranties of performance, merchantability or fitness for any particular
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19 # purpose.
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20 #
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21 # Please cite the author in any work or product based on this material.
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22 #
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23 # ===========================================================================
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24
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25
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26 The tool 'vdb-config' can be used to inspect or change the configuration
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27 of the sra-toolkit.
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28
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29 When called without any parameters the tool reports the current configuration
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30 in xml-format. No changes are made.
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31
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32 -----------------------------------------------------------------------------
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33
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34 vdb-config --restore-defaults
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35
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36 If called with this parameter the tool will bring the configuration into
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37 default state.
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38
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39 -----------------------------------------------------------------------------
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40
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41 vdb-config -i
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42
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43 This will present the user with a colored configuration dialog.
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44
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45 The tab-key and the cursor-keys navigate the dialog. The item with the little
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46 red square has the focus. A button or a checkbox can be 'pressed' with the
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47 space or enter-key. To get out of the dialog without saving any changes
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48 press the '6'-key or the 'q'-key or navigate to the 'exit'-button at the
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49 bottom of the dialog and press the space or enter-key.
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50
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51
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52 The "data source" part:
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53
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54 The "NCBI SRA" labeled checkbox enables/disables remote access to the SRA-
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55 accession stored at NCBI. As long as the computer has internet-access and this
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56 checkbox is enabled the user can access SRA-accessions directly without
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57 downloading them.
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58
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59 A command like 'sra-pileup SRR341578' at the command-line will produce pileup
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60 output of the given accession even if this accession has not been downloaded
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61 before.
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62 The tool will download the data on the fly from our servers.
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63
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64
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65 There might be a checkbox labeled "site" below the "NCBI-SRA" one. If this
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66 checkbox is not available you do not have a 'site'-installation of SRA-data.
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67 If it is visible you do have such a site-installation and you can disable
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68 access to this data.
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69
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70
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71 The "local workspaces" part:
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72
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73 At the top are 2 buttons "import dbGaP-project" and "set default import path".
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74
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75 If you are not using dbGaP-projects (The database of Genotypes and Phenotypes)
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76 you can ignore these 2 buttons.
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77
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78 The "import dbGaP-project" button presents you with another dialog to select
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79 a ngc-file. You can navigate the directories of your computer to find and
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80 select one of these files. By default the focus is in the files-list. It may
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81 be empty.
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82 Use the cursor-key: 'up' to focus the 'directories'-list. If you press enter
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83 on any of the listed directory-names you change into this directory.
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84 The '[ .. ]' entry brings you back into the parent directory. If you see
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85 ngc-files in the lower 'files'-list press the tab-key to switch to the
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86 'files'-list. Press enter on one of them to select this file for import. You
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87 will see a success-message if the import was performed without errors.
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88 On Windows you cannot switch from one drive-letter
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89 to another when selecting.
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90
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91 The "set default import path" gives you the opportunity to specify a different
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92 default location for dbGaP-projects - for instance if your home directory is
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93 not big enough. You can always change the location for your dbGaP-project
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94 after the import.
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95
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96
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97 Below the 2 buttons is a list of local repositories. If there are no
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98 dbGaP-projects this list has only one entry "Open Access Data". This is the
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99 location where accessions get downloaded and cached. You can change these
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100 locations if for instance your home directory where they are created by
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101 default does not have enough space.
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102 The change button brings up a directory-select dialog.
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103
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104 If you made any changes like enabling/disabling or changed a location, the
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105 change is only written to the configuration if you exit the dialog via the
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106 'save and exit' button.
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107
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108 -----------------------------------------------------------------------------
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109
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110
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111 vdb-config -i --interactive-mode textual
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112
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113 This will present the user with a purely textual and sequential dialog. It is
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114 intended to be used if the colored mode does not work, maybe because of
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115 console issues.