Mercurial > repos > charles_s_test > seqsero2
diff libs/sratoolkit.2.8.0-centos_linux64/README-vdb-config @ 3:38ad1130d077 draft
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author | charles_s_test |
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date | Mon, 27 Nov 2017 11:21:07 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/libs/sratoolkit.2.8.0-centos_linux64/README-vdb-config Mon Nov 27 11:21:07 2017 -0500 @@ -0,0 +1,115 @@ +# =========================================================================== +# +# 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.