Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ABySS Upstream-Contact: Shaun Jackman Source: https://github.com/bcgsc/abyss/releases License: BCCA-Academic Debian may redistribute this software package. . BC CANCER AGENCY SOFTWARE LICENSE AGREEMENT (ACADEMIC USE) CAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS. This License Agreement (the "Agreement") is a legal contract between you, your employer, educational institution or organization (collectively, "You") and the British Columbia Cancer Agency ("BCCA") with respect to the license of the software, including all associated documentation (collectively, the "Product"). . BCCA is willing to license the Product to You only if You accept the terms and conditions of this Agreement. By clicking on the "I ACCEPT" button, or by copying, downloading, accessing or otherwise using the Product, You automatically agree to be bound by the terms of this Agreement. IF YOU DO NOT WISH TO BE BOUND BY THE TERMS OF THIS AGREEMENT, DO NOT COPY, DOWNLOAD, ACCESS OR OTHERWISE USE THE PRODUCT. . 1. AUTHORITY: In the event that You are an educational institution or organization, Your representative who is clicking the "I ACCEPT" button, or otherwise copying, downloading, accessing or using the Product hereby, in their personal capacity, represents and warrants that they possess the legal authority to enter into this Agreement on Your behalf and to bind You to the terms of this Agreement. . 2. LICENSE TO USE: BCCA hereby grants to You a personal, non-exclusive, non-transferable, limited license to use the Product solely for internal, non-commercial use for non-profit research or educational purposes only on the terms and conditions contained in this Agreement. The Product may be installed at a single site at Your premises only. A copy of the Product installed on a single common machine or cluster of machines may be shared for internal use by Qualified Users only. In order to be a "Qualified User", an individual must be a student, researcher, professor, instructor or staff member of a non-profit educational institution or organization who uses the Product solely for non-profit research or educational purposes. . 3. RESTRICTIONS: You acknowledge and agree that You shall not, and shall not authorize any third party to: (a) make copies of the Product, except as provided in Section 2 and except for a single backup copy, and any such copy together with the original must be kept in Your possession or control; (b) modify, adapt, decompile, disassemble, translate into another computer language, create derivative works of, or otherwise reverse engineer the Product, or disclose any trade secrets relating to the Product, except as permitted in Section 5; (c) license, sublicense, distribute, sell, lease, transfer, assign, trade, rent or publish the Product or any part thereof and/or copies thereof, to any third party; (d) use the Product to process any data other than Your own; (e) use the Product or any part thereof for any commercial or for-profit purpose or any other purpose other than as permitted in Section 2; or (f) use, without its express permission, the name of BCCA. . 4. INTELLECTUAL PROPERTY RIGHTS: Subject to Section 5 below, all patents, copyrights, trade secrets, service marks, trademarks and other proprietary rights in or related to the Product and any improvements, modifications and enhancements thereof are and will remain the exclusive property of BCCA or its licensors. You agree that You will not, either during or after the termination of this Agreement, contest or challenge the title to or the intellectual property rights of BCCA or its licensors in the Product or any portion thereof. . 5. OWNERSHIP OF IMPROVEMENTS: In the event that the Product, in the form provided to You, includes source code (the "Source Code"), You are entitled to make improvements, modifications and enhancements to the Source Code (collectively, "Improvements") which Improvements are to be used by You for non-profit research and educational purposes only and You shall be the owner of those Improvements that You directly make and of all intellectual property rights to such Improvements, subject to the foregoing limits on Your use and distribution of such Improvements. You hereby grant to BCCA a perpetual, non-exclusive, worldwide, fully-paid, irrevocable license to use such Improvements for any purposes whatsoever, and to sublicense such Improvements including the right for third parties to sublicense the same, in perpetuity to the extent such rights are not limited in duration under applicable law, without identifying or seeking Your consent. Notwithstanding the foregoing, You acknowledge that BCCA and its licensors will retain or own all rights in and to any pre-existing code or other technology, content and data that may be incorporated in the Improvements. For greater certainty, this Section applies solely to the Source Code and shall not give You any rights with respect to the object code or any other portion or format of the Product which use, for greater certainty, is limited as set forth in this Agreement including as set out in Section 3(b) above. You acknowledge and agree that you will provide copies of Improvements to BCCA in such format as reasonably requested by BCCA at any time upon the request of BCCA. . 6. CONFIDENTIALITY: You acknowledge that the Product is and incorporates confidential and proprietary information developed, acquired by or licensed to BCCA. You will take all reasonable precautions necessary to safeguard the confidentiality of the Product, and will not disclose any information about the Product to any other person without BCCA's prior written consent. You will not allow the removal or defacement of any confidential or proprietary notice placed on the Product. You acknowledge that any breach of this Section 6 will cause irreparable harm to BCCA and its licensors. . 7. NO WARRANTIES: THIS PRODUCT IS PROVIDED TO YOU BY BCCA IN ORDER TO ALLOW YOU TO OBTAIN ACCESS TO LEADING ACADEMIC RESEARCH. THE PRODUCT IS PROVIDED TO YOU ON AN "AS IS" BASIS WITHOUT WARRANTY OF ANY KIND. NO WARRANTY, REPRESENTATION OR CONDITION EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION, ANY IMPLIED WARRANTY OR CONDITION OF MERCHANTABILITY, NON-INFRINGEMENT, PERFORMANCE, DURABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR USE SHALL APPLY. BCCA DOES NOT WARRANT THAT THE PRODUCT WILL OPERATE ON A CONTINUOUS OR TROUBLE FREE BASIS. . 8. LIMITATION OF LIABILITY: TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL THE AGGREGATE LIABILITY OF BCCA TO YOU EXCEED THE AMOUNT YOU HAVE PAID TO ACQUIRE THE PRODUCT ("MAXIMUM AMOUNT") AND WHERE YOU HAVE NOT PAID ANY AMOUNT FOR THE PRODUCT THEN THE MAXIMUM AMOUNT SHALL BE DEEMED TO BE CDN$100.00. IN NO EVENT SHALL BCCA BE LIABLE FOR ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL, OR SPECIAL DAMAGES, INCLUDING WITHOUT LIMITATION ANY DAMAGES FOR LOST PROFITS OR SAVINGS, REGARDLESS OF WHETHER THEY HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. EXCEPT TO THE EXTENT THAT THE LAWS OF A COMPETENT JURISDICTION REQUIRE LIABILITIES BEYOND AND DESPITE THESE LIMITATIONS, EXCLUSIONS AND DISCLAIMERS, THESE LIMITATIONS, EXCLUSIONS AND DISCLAIMERS SHALL APPLY WHETHER AN ACTION, CLAIM OR DEMAND ARISES FROM A BREACH OF WARRANTY OR CONDITION, BREACH OF CONTRACT, NEGLIGENCE, STRICT LIABILITY OR ANY OTHER KIND OF CIVIL OR STATUTORY LIABILITY CONNECTED WITH OR ARISING FROM THIS AGREEMENT. YOU AGREE THAT THE FOREGOING DISCLAIMER OF WARRANTIES AND LIMITATION OF LIABILITY ARE FAIR IN LIGHT OF THE NATURE OF THE RIGHTS GRANTED HEREIN AND THE AMOUNT OF FEES PAID BY YOU IN RESPECT OF THE PRODUCT. . 9. INDEMNITY: You will indemnify, defend and hold harmless BCCA, its board of directors, staff and agents from and against any and all liability, loss, damage, action, claim or expense (including attorney's fees and costs at trial and appellate levels) in connection with any claim, suit, action, demand or judgement (collectively, "Claim") arising out of, connected with, resulting from, or sustained as a result of Your use of the Product or the downloading of the Product, including without limitation, any Claim relating to infringement of BCCA's intellectual property rights or the intellectual property rights of any third party. . 10. SUPPORT AND MAINTENANCE: You acknowledge and agree that, unless and to the extent expressly agreed by BCCA in a separate written document, the Product is provided to You without any support or maintenance from BCCA and, for greater certainty, BCCA shall have no obligation to issue any update or upgrade to any Product. . 11. TERM: This Agreement is effective until terminated. You may terminate this Agreement at any time by ceasing use of the Product and destroying or deleting any copies of the Product. This Agreement will terminate immediately without notice from BCCA if You fail to comply with any provision of this Agreement. BCCA may terminate this Agreement at any time upon notice to you where BCCA determines, in its sole discretion, that any continued use of the Product could infringe the rights of any third parties. Upon termination of this Agreement, and in any event upon BCCA delivering You notice of termination, You shall immediately purge all Products from Your computer system(s), return to BCCA all copies of the Product that are in Your possession or control, and cease any further development of any Improvements. On any termination of this Agreement Sections 1, 4, 6, 7, 8, 9, 13 and 14 shall survive such termination. . 12. GOVERNMENT END USERS: Where any of the Product is used, duplicated or disclosed by or to the United States government or a government contractor or sub contractor, it is provided with RESTRICTED RIGHTS as defined in Title 48 CFR 52.227-19 and is subject to the following: Title 48 CFR 2.101, 52.227-19, 227.7201 through 227.7202-4, FAR 52.227-14, and FAR 52.227-19(c)(1-2) and (6/87), and where applicable, the customary software license, as described in Title 48 CFR 227-7202 with respect to commercial software and commercial software documentation including DFAR 252.227-7013, DFAR 252,227-7014, DFAR 252.227-7015 and DFAR 252.7018, all as applicable. . 13. USE OF THE DOWNLOAD SERVICE: You acknowledge and agree that you will be responsible for all costs, charges and taxes (where applicable) arising out of Your use of the Product and the downloading of the Product. You acknowledge that You are responsible for supplying any hardware or software necessary to use the Product pursuant to this Agreement. . 14. GENERAL PROVISIONS: (a) This Agreement will be governed by the laws of the Province of British Columbia, and the laws of Canada applicable therein, excluding any rules of private international law that lead to the application of the laws of any other jurisdiction. The United Nations Convention on Contracts for the International Sale of Goods (1980) does not apply to this Agreement. The courts of the Province of British Columbia shall have non-exclusive jurisdiction to hear any matter arising in connection with this Agreement. (b) USE OF THE PRODUCT IS PROHIBITED IN ANY JURISDICTION WHICH DOES NOT GIVE EFFECT TO THE TERMS OF THIS AGREEMENT. (c) You agree that no joint venture, partnership, employment, consulting or agency relationship exists between You and BCCA as a result of this Agreement or Your use of the Product. (d) You hereby consent to Your contact information and any other personally identifiable information that You provide to us being disclosed to and maintained and used by us and our business partners for the purposes of (i) managing and developing our respective businesses and operations; (ii) marketing products and services to You and your staff; and (iii) developing new and enhancing existing products. You further agree that we may provide this information to other persons as required to satisfy any legal requirements and to any person that acquires some or all of the assets of BCCA. Where any of the personally identifiable information that You provide to us is in respect of individuals other than Yourself (such as Your staff) then You represent and warrant to use that You have obtained all necessary consents and authorizations from such individuals in order to comply with this provision. Please see the BCCA website for further information regarding personally identifiable information. (e) This Agreement is the entire Agreement between You and BCCA relating to this subject matter. You will not contest the validity of this Agreement merely because it is in electronic form. No modification of this Agreement will be binding, unless in writing and accepted by an authorized representative of each party. (f) The provisions of this Agreement are severable in that if any provision in the Agreement is determined to be invalid or unenforceable under any controlling body of law, that will not affect the validity or enforceability of the remaining provisions of the Agreement. (g) You agree to print out or download a copy of this Agreement and retain it for Your records. (h) You consent to the use of the English language in this Agreement. (i) You may not assign this Agreement or any of Your rights or obligations hereunder without BCCA's prior written consent. BCCA, at its sole discretion may assign this Agreement without notice to You. Files: * Copyright: Copyright 2013 Genome Sciences Centre License: BCCA-Academic Files: Common/* DistanceEst/* ParseAligns/* Copyright: Copyright 2012 Genome Sciences Centre License: BCCA-Academic or GPL-3+ Files: Common/cholesky.hpp Copyright: Copyright 2005 Gunter Winkler, Konstantin Kutzkow License: LGPL-2.1+ Files: Common/city.cc Common/city.h Copyright: Copyright 2011 Google, Inc. License: Expat Files: dialign/* Copyright: Copyright 2008 Amarendran R. Subramanian License: LGPL-2.1+ License: LGPL-2.1+ On Debian systems, see `/usr/share/common-licenses/LGPL-2.1'. . This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library 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 Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA . Amarendran R. Subramanian, hereby disclaims all copyright interest in the DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian. . Amarendran R. Subramanian, 2004-2008 . DIALIGN-TX has been co-authored by Volker Menrad and Dorothea Emig. . Research work using DIALIGN-TX should cite: . DIALIGN-TX: improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern, Algorithms for Molecular Biology 3:6, 2008 . DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005 Files: FMIndex/bit_array.h Copyright: Copyright 2010 Daisuke Okanohara License: BSD-3-clause 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 authors nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. Files: FMIndex/sais.hxx Copyright: Copyright 2010 Yuta Mori License: Expat License: Expat 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. License: GPL-3+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. . This program 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 for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.