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

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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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.