Update user manual

Author: Lenbok

installer/resources/core/RTGOperationsManual.pdf

@@ -6,11 +6,7 @@ Advanced installation configuration
 
 RTG software can be shared by a group of users by installing on a
 centrally available file directory or shared drive. Assignment of
-execution privileges can be determined by the administrator, independent
-of the software license file. For commercial users, the software license
-prepared by Real Time Genomics (``rtg-license.txt``) need only be included
-in the same directory as the executable (``RTG.jar``) and the run-time
-scripts (``rtg`` or ``rtg.bat``).
+execution privileges can be determined by the administrator.
 
 During installation on Unix systems, a configuration file named
 ``rtg.cfg`` is created in the installation directory. By editing this
@@ -138,15 +134,13 @@ Usage logging
 RTG has the ability to record simple command usage information for
 submission to Real Time Genomics. The first time RTG is run (typically
 during installation), the user will be asked whether to enable usage
-logging. This information may be required for customers with a
-pay-per-use license. Other customers may choose to send this information
+logging. Customers may choose to send this information
 to give Real Time Genomics feedback on which commands and features are
 commonly used or to locally log RTG command use for their own analysis.
 
 A usage record contains the following fields:
 
 -  Time and date
--  License serial number
 -  Unique ID for the run
 -  Version of RTG software
 -  RTG command name, without parameters (e.g. map)

installer/resources/core/RTGOperationsManual/_sources/administration.rst.txt

@@ -323,6 +323,10 @@ for files from third party sources or RTG command output where the
 
   .. include:: appendix_output_formats.inc.rst
 
+.. only:: extra
+
+  .. include:: appendix/segment_output_formats.inc.rst
+
 RTG JavaScript filtering API
 ----------------------------
 
@@ -507,7 +511,7 @@ present. This will add an ``FILTER`` declaration line to the header.
 
 .. code-block:: javascript
 
-  ensureFilterHeader('##INFO=<ID=FAIL_VAL,' +
+  ensureFilterHeader('##FILTER=<ID=FAIL_VAL,' +
     'Description="Failed validation">');
 
 
@@ -661,7 +665,7 @@ notice. While every effort has been made to make this guide as complete
 and accurate as possible as of the publication date, no warranty of
 fitness is implied.
 
-© 2017 Real Time Genomics All rights reserved.
+© 2025 Real Time Genomics All rights reserved.
 
 Illumina, Solexa, Complete Genomics, Ion Torrent, Roche, ABI, Life
 Technologies, and PacBio are registered trademarks and all other brands

installer/resources/core/RTGOperationsManual/_sources/appendix.rst.txt

@@ -29,8 +29,8 @@ RTG software description
 
 RTG software is delivered as a single executable with multiple commands
 executed through a command line interface (CLI). Commands are delivered
-in product packages, and for commercial users each command can be
-independently enabled through a license key.
+in product packages, and the available commands vary per product
+package.
 
 Usage:
 
@@ -115,10 +115,7 @@ Here are platform-specific instructions for RTG deployment.
 Linux/MacOS X:
 
 -  Unzip the RTG distribution to the desired location.
--  If your installation requires a license file (``rtg-license.txt``),
-   copy the license file provided by Real Time Genomics into the RTG
-   distribution directory.
-- In a terminal, cd to the installation directory and test for success
+-  In a terminal, cd to the installation directory and test for success
    by entering ``./rtg version``
 -  On MacOS X, depending on your operating system version and
    configuration regarding unsigned applications, you may encounter the
@@ -156,9 +153,6 @@ Linux/MacOS X:
 Windows:
 
 -  Unzip the RTG distribution to the desired location.
--  If your installation requires a license, copy the license file
-   provided by Real Time Genomics (``rtg-license.txt``) into the RTG
-   distribution directory.
 -  Test for success by entering ``rtg version`` at the command line. The
    first time RTG is executed you will be prompted with some questions
    to customize your installation. Follow the prompts.
@@ -170,25 +164,6 @@ Windows:
    override this limit by setting the ``RTG_MEM`` variable in the
    ``rtg.bat`` script or as an environment variable.
 
-License Management
-~~~~~~~~~~~~~~~~~~
-
-Commercial distributions of RTG products require the presence of a valid
-license key file for operation.
-
-The license key file must be located in the same directory as the RTG
-executable. The license enables the execution of a particular command
-set for the purchased product(s) and features.
-
-A license key allows flexible use of the RTG package on any node or CPU
-core.
-
-To view the current license features at the command prompt, enter:
-
-.. code-block:: text
-
-  $ rtg license
-
 .. seealso:: For more data center deployment and instructions for
   editing scripts, see :ref:`Administration & capacity planning`.
 

installer/resources/core/RTGOperationsManual/_sources/overview.rst.txt

@@ -15,10 +15,7 @@ RTG is installed as a single executable in any system subdirectory where
 permissions authorize a particular community of users to run the
 application. RTG commands are executed through the RTG command-line
 interface (CLI). Each command has its own set of parameters and options
-described in this section. The availability of each command may be
-determined by the RTG license that has been installed. Contact
-``[email protected]`` to discuss changing the set of commands
-that are enabled by your license.
+described in this section.
 
 Results are organized in results directories defined by command
 parameters and settings. The command line shell environment should
@@ -134,16 +131,15 @@ launch of RTG product commands, options, and utilities:
   $ rtg version
 
 It will display the version of the RTG software installed, RAM
-requirements, and license expiration, for example:
+requirements, for example:
 
 .. code-block:: text
 
   $rtg version
   Product: RTG Core 3.5
   Core Version: 6236f4e (2014-10-31)
   RAM: 40.0GB of 47.0GB RAM can be used by rtg (84%)
-  License: Expires on 2015-09-30
-  License location: /home/rtgcustomer/rtg/rtg-license.txt
+  License: No license file required
   Contact: [email protected]
 
   Patents / Patents pending:
@@ -163,14 +159,12 @@ requirements, and license expiration, for example:
   doi:10.1089/cmb.2014.0029.
   (c) Real Time Genomics Inc, 2014
 
-To see what commands you are licensed to use, type ``rtg license``:
+To see release status of commands you are licensed to use, type ``rtg license``:
 
 .. code-block:: text
 
   $rtg license
-  License: Expires on 2015-03-30
-  Licensed to: John Doe
-  License location: /home/rtgcustomer/rtg/rtg-license.txt
+  License: No license file required
 
       Command name    Licensed?  Release Level
 
@@ -285,8 +279,7 @@ license, type ``rtg help``:
         license                print license information for all commands
         help                   print this screen or help for specified command
 
-The help command will only list the commands for which you have a
-license to use.
+The help command will only list the commands at GA or beta release level.
 
 To display help and syntax information for a specific command from the
 command line, type the command and then the --help option, as in:
@@ -307,6 +300,21 @@ command line, type the command and then the --help option, as in:
 
   .. include:: rtg_command_reference_mapish.inc.rst
 
+.. only:: core or extra
+
+  .. include:: rtg_command_reference_variant_calling.inc.rst
+
+  .. only:: extra
+
+    .. include:: rtg_command_reference/segment.inc.rst
+    .. include:: rtg_command_reference/cnvsummary.inc.rst
+    .. include:: rtg_command_reference/cnvponbuild.inc.rst
+    .. include:: rtg_command_reference/fusionfilter.inc.rst
+
+.. only:: core or extra
+
+  .. include:: rtg_command_reference_metagenomics.inc.rst
+
 .. include:: rtg_command_reference_simulation.inc.rst
 
 .. include:: rtg_command_reference_utility.inc.rst