X!TANDEM LICENSE AND README ===========================================


 X! tandem protein sequence modeler

  What is it?
  -----------
  X! tandem open source software that can model tandem
  mass spectra with protein sequences. This software
  has a very simple, unsophistocated application programming
  interface (API): it simply takes an XML file of instructions
  on its command line, and output the results into an XML file,
  which has been specified in the input XML file. 
  
  The Latest Version
  ------------------

  Details of the latest version can be found on the X! tandem
  project page under http://www.thegpm.org. 
  This version is the first release the CYCLONE edition (version 2012.10.01.1).


  Documentation
  -------------

  This version of X! tandem is a full release, only including source
  level documentation. As more releases occur, better documentation
  will be included.

  Installation
  ------------

  (IN this case installation is automatically done by Galaxy's Toolshed).

  Licensing
  ---------

	The Artistic License for all X! software, binaries and documentation

	Preamble
	The intent of this document is to state the conditions under which a
	Package may be copied, such that the Copyright Holder maintains some 
	semblance of artistic control over the development of the package, 
	while giving the users of the package the right to use and distribute 
	the Package in a more-or-less customary fashion, plus the right to 
	make reasonable modifications. 

	Definitions
	"Package" refers to the collection of files distributed by the Copyright 
	  Holder, and derivatives of that collection of files created through 
	  textual modification. 

	"Standard Version" refers to such a Package if it has not been modified, 
	  or has been modified in accordance with the wishes of the Copyright 
	  Holder as specified below. 

	"Copyright Holder" is whoever is named in the copyright or copyrights 
	  for the package. 

	"You" is you, if you're thinking about copying or distributing this Package. 

	"Reasonable copying fee" is whatever you can justify on the basis of 
	  media cost, duplication charges, time of people involved, and so on. 
	  (You will not be required to justify it to the Copyright Holder, but 
	  only to the computing community at large as a market that must bear 
	  the fee.) 

	"Freely Available" means that no fee is charged for the item itself, 
	  though there may be fees involved in handling the item. It also means 
	  that recipients of the item may redistribute it under the same
	  conditions they received it. 

	1. You may make and give away verbatim copies of the source form of the 
	Standard Version of this Package without restriction, provided that 
	you duplicate all of the original copyright notices and associated 
	disclaimers. 

	2. You may apply bug fixes, portability fixes and other modifications 
	derived from the Public Domain or from the Copyright Holder. A 
	Package modified in such a way shall still be considered the Standard 
	Version. 

	3. You may otherwise modify your copy of this Package in any way, provided 
	that you insert a prominent notice in each changed file stating how and 
	when you changed that file, and provided that you do at least ONE of the 
	following: 

	  a. place your modifications in the Public Domain or otherwise make them 
		 Freely Available, such as by posting said modifications to Usenet 
		 or an equivalent medium, or placing the modifications on a major 
		 archive site such as uunet.uu.net, or by allowing the Copyright Holder 
		 to include your modifications in the Standard Version of the Package. 
	  b. use the modified Package only within your corporation or organization. 
	  c. rename any non-standard executables so the names do not conflict 
		 with standard executables, which must also be provided, and provide 
		 a separate manual page for each non-standard executable that clearly 
		 documents how it differs from the Standard Version. 
	  d. make other distribution arrangements with the Copyright Holder. 

	4. You may distribute the programs of this Package in object code or 
	executable form, provided that you do at least ONE of the following: 

	  a. distribute a Standard Version of the executables and library files, 
		 together with instructions (in the manual page or equivalent) on 
		 where to get the Standard Version. 
	  b. accompany the distribution with the machine-readable source of the 
		 Package with your modifications. 
	  c. give non-standard executables non-standard names, and clearly 
		 document the differences in manual pages (or equivalent), together 
		 with instructions on where to get the Standard Version. 
	  d. make other distribution arrangements with the Copyright Holder. 

	5. You may charge a reasonable copying fee for any distribution of 
	this Package. You may charge any fee you choose for support of 
	this Package. You may not charge a fee for this Package itself. 
	However, you may distribute this Package in aggregate with other 
	(possibly commercial) programs as part of a larger (possibly 
	commercial) software distribution provided that you do not a
	dvertise this Package as a product of your own. You may embed this 
	Package's interpreter within an executable of yours (by linking); 
	this shall be construed as a mere form of aggregation, provided that 
	the complete Standard Version of the interpreter is so embedded. 

	6. The scripts and library files supplied as input to or produced as 
	output from the programs of this Package do not automatically fall 
	under the copyright of this Package, but belong to whomever generated 
	them, and may be sold commercially, and may be aggregated with this 
	Package. If such scripts or library files are aggregated with this 
	Package via the so-called "undump" or "unexec" methods of producing 
	a binary executable image, then distribution of such an image shall 
	neither be construed as a distribution of this Package nor shall it 
	fall under the restrictions of Paragraphs 3 and 4, provided that you 
	do not represent such an executable image as a Standard Version of 
	this Package. 

	7. C subroutines (or comparably compiled subroutines in other languages) 
	supplied by you and linked into this Package in order to emulate 
	subroutines and variables of the language defined by this Package 
	shall not be considered part of this Package, but are the equivalent 
	of input as in Paragraph 6, provided these subroutines do not change 
	the language in any way that would cause it to fail the regression 
	tests for the language. 

	8. Aggregation of this Package with a commercial distribution is always 
	permitted provided that the use of this Package is embedded; that is, 
	when no overt attempt is made to make this Package's interfaces visible 
	to the end user of the commercial distribution. Such use shall not be 
	construed as a distribution of this Package. 

	9. The name of the Copyright Holder may not be used to endorse or promote 
	products derived from this software without specific prior written permission. 

	10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED 
	WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF 
	MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. 

	The End 


  Contacts
  --------

  For any questions involving X! tandem, please contact 
  contact@thegpm.org

  Acknowledgments
  ----------------

  Ron Beavis - system design and implementation
  Rob Craig - debugging and LINUX implementation
  Jayson Falkner - code for GeeToo LINUX implementation
  Patrick Lacasse - initial additions for mzxml and mzdata functionality
  Brendan McLean - optimized changes for mzxml and mzdata functionality using expat library