Add license and startup script

Author: julianhess

LICENSE

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+By downloading the PROGRAM you agree to the following terms of use:
+
+BROAD INSTITUTE SOFTWARE LICENSE AGREEMENT
+FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+
+This Agreement is made between the Broad Institute, Inc. with a principal 
+address at 7 Cambridge Center, Cambridge, MA 02142 ("BROAD") and the 
+LICENSEE and is effective at the date the downloading is completed 
+("EFFECTIVE DATE").
+WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, 
+and BROAD wishes to have this PROGRAM utilized in the public interest, 
+subject only to the royalty-free, nonexclusive, nontransferable license 
+rights of the United States Government pursuant to 48 CFR 52.227-14; and
+WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant 
+a license on the following terms and conditions.
+NOW, THEREFORE, in consideration of the promises and covenants made herein, 
+the parties hereto agree as follows:
+
+1. DEFINITIONS
+1.1	"PROGRAM" shall mean copyright in the object code and source code 
+known as MutSig and related documentation, if any, as they exist on the 
+EFFECTIVE DATE and can be downloaded from 
+http://www.broadinstitute.org/cancer/cga/MutSig on the EFFECTIVE DATE.
+
+2. LICENSE
+2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to 
+LICENSEE, solely for academic non-commercial research purposes, a non-
+exclusive, non-transferable license to: (a) download, execute and display 
+the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+
+LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-
+free, irrevocable license to any LICENSEE bug fixes or modifications to the 
+PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE 
+agrees to provide any such modifications and bug fixes to BROAD promptly 
+upon their creation.
+
+The LICENSEE may apply the PROGRAM in a pipeline to data owned by users 
+other than the LICENSEE and provide these users the results of the PROGRAM 
+provided LICENSEE does so for academic non-commercial purposes only.  For 
+clarification purposes, academic sponsored research is not a commercial use 
+under the terms of this Agreement.
+
+2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or 
+distribute the PROGRAM, in whole or in part, without prior written 
+permission from BROAD.  LICENSEE shall ensure that all of its users agree 
+to the terms of this Agreement.  LICENSEE further agrees that it shall not 
+put the PROGRAM on a network, server, or other similar technology that may 
+be accessed by anyone other than the LICENSEE and its employees and users 
+who have agreed to the terms of this agreement.
+
+2.3  License Limitations. Nothing in this Agreement shall be construed to 
+confer any rights upon LICENSEE by implication, estoppel, or otherwise to 
+any computer software, trademark, intellectual property, or patent rights 
+of BROAD, or of any other entity, except as expressly granted herein. 
+LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for 
+any commercial purpose, including without limitation, as the basis of a 
+commercial software or hardware product or to provide services. LICENSEE 
+further agrees that the PROGRAM shall not be copied or otherwise adapted in 
+order to circumvent the need for obtaining a license for use of the 
+PROGRAM.  
+
+3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. 
+The PROGRAM is marked with the following BROAD copyright notice and notice 
+of attribution to contributors. LICENSEE shall retain such notice on all 
+copies.  LICENSEE agrees to include appropriate attribution if any results 
+obtained from use of the PROGRAM are included in any publication.
+
+Copyright 2012 Broad Institute, Inc.
+Notice of attribution:  The MutSig program was made available through the 
+generosity of the Cancer Genome Analysis group at the Broad Institute, Inc. 
+
+LICENSEE shall not use any trademark or trade name of BROAD, or any 
+variation, adaptation, or abbreviation, of such marks or trade names, or 
+any names of officers, faculty, students, employees, or agents of BROAD 
+except as states above for attribution purposes.
+
+4. INDEMNIFICATION
+LICENSEE shall indemnify, defend, and hold harmless BROAD, and their 
+respective officers, faculty, students, employees, associated investigators 
+and agents, and their respective successors, heirs and assigns, 
+("Indemnitees"), against any liability, damage, loss, or expense (including 
+reasonable attorneys fees and expenses) incurred by or imposed upon any of 
+the Indemnitees in connection with any claims, suits, actions, demands or 
+judgments arising out of any theory of liability (including, without 
+limitation, actions in the form of tort, warranty, or strict liability and 
+regardless of whether such action has any factual basis) pursuant to any 
+right or license granted under this Agreement.
+
+5. NO REPRESENTATIONS OR WARRANTIES
+THE PROGRAM IS DELIVERED "AS IS."  BROAD MAKES NO REPRESENTATIONS OR 
+WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR 
+IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, 
+FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT 
+OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES 
+OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER 
+LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, 
+AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR 
+CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC 
+DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD 
+SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF 
+THE POSSIBILITY OF THE FOREGOING.
+
+6. ASSIGNMENT
+This Agreement is personal to LICENSEE and any rights or obligations 
+assigned by LICENSEE without the prior written consent of BROAD shall be 
+null and void.
+
+7. MISCELLANEOUS
+7.1 Export Control. LICENSEE gives assurance that it will comply with all 
+United States export control laws and regulations controlling the export of 
+the PROGRAM, including, without limitation, all Export Administration 
+Regulations of the United States Department of Commerce. Among other 
+things, these laws and regulations prohibit, or require a license for, the 
+export of certain types of software to specified countries.
+7.2 Termination. LICENSEE shall have the right to terminate this Agreement 
+for any reason upon prior written notice to BROAD. If LICENSEE breaches any 
+provision hereunder, and fails to cure such breach within thirty (30) days, 
+BROAD may terminate this Agreement immediately. Upon termination, LICENSEE 
+shall provide BROAD with written assurance that the original and all copies 
+of the PROGRAM have been destroyed, except that, upon prior written 
+authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+7.3 Survival. The following provisions shall survive the expiration or 
+termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 
+7.3, and 7.4.
+7.4 Notice. Any notices under this Agreement shall be in writing, shall 
+specifically refer to this Agreement, and shall be sent by hand, recognized 
+national overnight courier, confirmed facsimile transmission, confirmed 
+electronic mail, or registered or certified mail, postage prepaid, return 
+receipt requested.  All notices under this Agreement shall be deemed 
+effective upon receipt. 
+7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, 
+supplemented, or otherwise modified only by means of a written instrument 
+signed by all parties. Any waiver of any rights or failure to act in a 
+specific instance shall relate only to such instance and shall not be 
+construed as an agreement to waive any rights or fail to act in any other 
+instance, whether or not similar. This Agreement constitutes the entire 
+agreement among the parties with respect to its subject matter and 
+supersedes prior agreements or understandings between the parties relating 
+to its subject matter. 
+7.6 Binding Effect; Headings. This Agreement shall be binding upon and 
+inure to the benefit of the parties and their respective permitted 
+successors and assigns. All headings are for convenience only and shall not 
+affect the meaning of any provision of this Agreement.
+7.7 Governing Law. This Agreement shall be construed, governed, interpreted 
+and applied in accordance with the internal laws of the Commonwealth of 
+Massachusetts, U.S.A., without regard to conflict of laws principles.

startup.m

@@ -0,0 +1,4 @@
+if ~isdeployed
+  restoredefaultpath
+  addpath src
+end