Merge pull request #315 from marbre/trans-abyss

sci-biology/trans-abys: Fix license and keywords

2 files changed, 456 insertions, 2 deletions

diff --git a/licenses/bcca_2010 b/licenses/bcca_2010
new file mode 100644
index 000000000..c8874f8c5
--- /dev/null
+++ b/licenses/bcca_2010
@@ -0,0 +1,453 @@
+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.
\ No newline at end of file
diff --git a/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
index c8538cb9a..9d6a25055 100644
--- a/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
+++ b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
@@ -8,9 +8,10 @@ DESCRIPTION="Analyze and combine multiple assemblies from abyss"
 HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss"
 SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/"${PV}"/trans-ABySS-v"${PV}"_20130916.tar.gz"
 
-LICENSE=""
+# http://www.bcgsc.ca/platform/bioinfo/license/bcca_2010
+LICENSE="bcca_2010"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~x86 ~amd64"
 IUSE=""
 
 # perl and python