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NOTICE
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Please report bugs to:
Alexie Papanicolaou
Hawkesbury Institute for the Environment, Western Sydney University, Richmond NSW, Australia
=============================================================================================================
LEGALESE
LICENSE
This software is released under the terms specified in LICENSE file. This Open-Source LICENSE gives you
certain rights under certain terms for using the software, please respect them.
This software contains or links code from the following software each of which may fall under a particular notice:
== The following tools contributed code which may have been modified.
PASA (PerlLib)
==============
http://pasa.sourceforge.net/
Copyright (c) 2012, The Broad Institute, Inc. All rights reserved.
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 Broad 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 BROAD INSTITUTE ''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 BROAD INSTITUTE
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.
== The following tools are linked/aggregated without modifications unless mentioned:
biokanga
=======
see https://sourceforge.net/projects/biokanga/
Licensed under the Apache License, Version 2.0 (the "License");
CanvasXpress
============
http://canvasxpress.org
Commercial License to CSIRO (otherwise GPL for all other users)
CanvasXpress is licensed under a commercial license to CSIRO
You may use the CanvasXpress files in this application only if you don't modify ANY of the code here.
If you wish to modify this code, you must download an open source license from CanvasXpress.
express
=======
Artistic License 2.0
Samtools
========
http://samtools.sourceforge.net/
We modified the Makefile to not install the LIBCURSES GUI
Distributed under GPL's aggregation terms:
A compilation of a covered work with other separate and independent
works, which are not by their nature extensions of the covered work,
and which are not combined with it such as to form a larger program,
in or on a volume of a storage or distribution medium, is called an
"aggregate" if the compilation and its resulting copyright are not
used to limit the access or legal rights of the compilation's users
beyond what the individual works permit. Inclusion of a covered work
in an aggregate does not cause this License to apply to the other
parts of the aggregate. [http://www.gnu.org/licenses/gpl.html]
Bedtools
========
Distributed under GPL's aggregation terms
http://code.google.com/p/bedtools