========================================================================= _____ _ _ ___ __ __ | ___ \ \ | |/ _ \ \ \ / / | |_/ / \| / /_\ \ ___ \ V / _ __ _ __ ___ ___ ___ | /| . ` | _ | / _ \/ \| '_ \| '__/ _ | __/ __| | |\ \| |\ | | | | | __/ /^\ \ |_) | | | __|__ \__ \ \_| \_\_| \_|_| |_/ \___\/ \/ .__/|_| \___|___/___/ | | |_| http://www.rnaexpress.org/ ========================================================================= Copyright 2012, Sam Forster, Alex Finkel, Jodee Gould and Paul Hertzog. RNA eXpress is a RNA-Seq analysis program developed at the Monash Institute of Medical Research, Monash University, Australia. Contact: Prof. Paul Hertzog, Centre for Innate Immunity and Infectious Diseases Monash Institute of Medical Research 27 - 31 Wright Street, Clayton, VIC 3169 Australia paul.hertzog@monash.edu ------------------- ACKNOWLEDGEMENTS ------------------- The authors would like to acknowledge the support and contributions of Bio21 Undergraduate Research Opportunities Program, National Health and Medical Research Council, Monash e-Research, the ARC Centre of Excellence in Structural and Functional Microbial Genomics and the Victorian Government's Operational Infrastructure Support Program ------------------- News ------------------- Version 1.2 represents the second major public release of RNA eXpress. More information, tutorials, new algorithms and licensing is available at http://www.rnaexpress.org/ ------------------- Install ------------------- RNA eXpress requires Java 1.6 or greater to run. After installing Java RNA eXpress can be run using the following command java -jar rnaexpress--.jar where: is replaced by either windows, linux or mac is replaced by the current version. e.g. 1.0 If you encounter out of memory exceptions the memory can be increased using the -Xmx flag at runtime. For example to use 4G of memory the following command would be used: java -jar -Xmx4000M rnaexpress--.jar With particularly large amounts of sequencing a StackOverflow exception may occur. If you encouter this error your Java environment can be modified to increase the thread stack size using the -Xss flag. For example to use 10M stack size use the following command java -jar -Xss10M rnaexpress--.jar Alteratively the .sh, .bat or .app files can be used to execute the program on linux, windows, and mac respectively. The command line runtime options are as follows: No options runs the GUI with default parameters. OPTIONS: java -jar rnaexpress--.jar config_file ----> Run the GUI, loading settings from config_file. java -jar rnaexpress--.jar -n config_file ----> Run Express immediately from the config_file without loading the GUI java -jar rnaexpress--.jar -h -help --help ----> Display this message in the command line. For comprehensive installation guide, tutorials and configuration file parameters see the user guide. To ask for help, please post a question at http://www.rnaexpress.org/forum ------------------- COPYING / LICENSE ------------------- RNA eXpress is distributed under a "license for purpose" model: - Academic and private users are granted source code access under the GPL 3.0 license. Details of the restrictions placed by this license can be found in the COPYING file included with this download. - Compiled binaries are provided 'as is' by Monash Institute for use by Monash researchers and their research collaborators at other institutions. Monash University does not warrant the accuracy of the information provided by the application, nor the fitness for purpose of the application for your intended usage. Services are provided to 3rd parties on an 'all care no responsibility' basis. - Neither of these agreements are applicable for commercial entities. Commercial users or users gaining commercial benefit from the use of this software are not entitled to download or use binaries or source code from RNA eXpress without first receiving permission from the authors directly in writing.