=== RTG Tools === RTG software from Real Time Genomics includes tools for the processing and analysis of plant, animal and human sequence data from high throughput sequencing systems. Product usage and administration is described in the accompanying RTG Operations Manual. Quick Start Instructions ======================== RTG software is delivered as a command-line Java application accessed via a wrapper script that allows a user to customize initial memory allocation and other configuration options. It is recommended that these wrapper scripts be used rather than directly accessing the Java JAR. For individual use, follow these quick start instructions. No-JRE: The no-JRE distribution does not include a Java Runtime Environment and instead uses the system-installed Java. Ensure that at the command line you can enter 'java -version' and that this command reports a java version of 1.8 or higher before proceeding with the steps below. This may require setting your PATH environment variable to include the location of an appropriate version of java. Linux/MacOS X: Unzip the RTG distribution to the desired location. If your RTG 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 by entering './rtg version' On MacOS X, depending on your operating system version and configuration regarding unsigned applications, you may encounter the error message: -bash: rtg: /usr/bin/env: bad interpreter: Operation not permitted If this occurs, you must clear the OS X quarantine attribute with the command: xattr -d com.apple.quarantine rtg The first time rtg is executed you will be prompted with some questions to customize your installation. Follow the prompts. Enter './rtg help' for a list of rtg commands. Help for any individual command is available using the --help flag, e.g.: './rtg format --help' By default, RTG software scripts establish a memory space of 90% of the available RAM - this is automatically calculated. One may override this limit in the rtg.cfg settings file or on a per-run basis by supplying RTG_MEM as an environment variable or as the first program argument, e.g.: './rtg RTG_MEM=48g map' [OPTIONAL] If you will be running rtg on multiple machines and would like to customize settings on a per-machine basis, copy rtg.cfg to /etc/rtg.cfg, editing per-machine settings appropriately (requires root privileges). An alternative that does not require root privileges is to copy rtg.example.cfg to rtg.HOSTNAME.cfg, editing per-machine settings appropriately, where HOSTNAME is the short host name output by the command "hostname -s" Windows: Unzip the RTG distribution to the desired location. If your RTG distribution requires a license file (rtg-license.txt), copy the license file from Real Time Genomics 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. Enter 'rtg help' for a list of rtg commands. Help for any individual command is available using the --help flag, e.g.: 'rtg format --help' By default, RTG software scripts establish a memory space of 90% of the available RAM - this is automatically calculated. One may override this limit by setting the RTG_MEM variable in the rtg.bat script or as an environment variable. The scripts subdirectory contains demos, helper scripts, and example configuration files, and comprehensive documentation is contained in the RTG Operations Manual. Using the above quick start installation steps, an individual can execute RTG software in a remote computing environment without the need to establish root privileges. Include the necessary data files in directories within the workspace and upload the entire workspace to the remote system (either stand-alone or cluster). For data center deployment and instructions for editing scripts, please consult the Administration chapter of the RTG Operations Manual. A discussion group is now available for general questions, tips, and other discussions. It may be viewed or joined at: https://groups.google.com/a/realtimegenomics.com/forum/#!forum/rtg-users To be informed of new software releases, subscribe to the low-traffic rtg-announce group at: https://groups.google.com/a/realtimegenomics.com/forum/#!forum/rtg-announce Citing RTG ========== John G. Cleary, Ross Braithwaite, Kurt Gaastra, Brian S. Hilbush, Stuart Inglis, Sean A. Irvine, Alan Jackson, Richard Littin, Sahar Nohzadeh-Malakshah, Mehul Rathod, David Ware, Len Trigg, and Francisco M. De La Vega. "Joint Variant and De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data." Journal of Computational Biology. June 2014, 21(6): 405-419. doi:10.1089/cmb.2014.0029. Terms of Use ============ This proprietary software program is the property of Real Time Genomics. All use of this software program is subject to the terms of an applicable end user license agreement. Patents ======= US: 7,640,256, 13/129,329, 13/681,046, 13/681,215, 13/848,653, 13/925,704, 14/015,295, 13/971,654, 13/971,630, 14/564,810 UK: 1222923.3, 1222921.7, 1304502.6, 1311209.9, 1314888.7, 1314908.3 New Zealand: 626777, 626783, 615491, 614897, 614560 Australia: 2005255348, Singapore: 128254 Other patents pending Third Party Software Used ========================= RTG software uses the open source htsjdk library (https://github.com/samtools/htsjdk) for reading and writing SAM files, under the terms of following license: The MIT License Copyright (c) 2009 The Broad Institute Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ------------------------- RTG software uses the bzip2 library included in the open source Ant project (http://ant.apache.org/) for decompressing bzip2 format files, under the following license: Copyright 1999-2010 The Apache Software Foundation Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. ------------------------- RTG Software uses a modified version of java/util/zip/GZIPInputStream.java (available in the accompanying gzipfix.jar) from OpenJDK 7 under the terms of the following license: This code is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 only, as published by the Free Software Foundation. Oracle designates this particular file as subject to the "Classpath" exception as provided by Oracle in the LICENSE file that accompanied this code. This code is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License version 2 for more details (a copy is included in the LICENSE file that accompanied this code). You should have received a copy of the GNU General Public License version 2 along with this work; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA or visit www.oracle.com if you need additional information or have any questions. ------------------------- RTG Software uses hierarchical data visualization software from http://sourceforge.net/projects/krona/ under the terms of the following license: Copyright (c) 2011, Battelle National Biodefense Institute (BNBI); all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and Adam Phillippy This Software was prepared for the Department of Homeland Security (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as part of contract HSHQDC-07-C-00020 to manage and operate the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the Battelle National Biodefense Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.