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Extracted code for RTG Core, truncate history
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‎.gitignore

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# git ls-files --others --exclude-from=.git/info/exclude
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# Lines that start with '#' are comments.
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# For a project mostly in C, the following would be a good set of
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# exclude patterns (uncomment them if you want to use them):
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# *.[oa]
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# *~
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*.class
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*.aux
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*.log
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*.dvi
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*.pdf
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*.ps
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*.eps
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*.swp
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*.el
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*~
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#*#
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.#.*
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out
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bin
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build
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dist
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tmp
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.ant-targets-build.xml
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.settings
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*.classpath
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*.project
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/test/.checkstyle
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/.metadata
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/.idea
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*.iml

‎LICENSE.txt

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SOFTWARE LICENSE AGREEMENT
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(ACADEMIC NON-COMMERCIAL RESEARCH)
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PARTIES
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1 REAL TIME GENOMICS LIMITED, of New Zealand (RTG)
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2 USER (User)
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BACKGROUND
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RTG owns and has intellectual property rights (including patents and
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patents pending) in certain software applications that enable
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processing and analysis of genomic data. RTG wishes to make available
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those applications and their source code for non-commercial use within
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the academic research community, on a royalty-free basis. This
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License Agreement sets out the terms on which RTG makes those
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applications, that source code and any accompanying documentation
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available for academic non-commercial research.
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1. INTERPRETATION
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1.1. Definitions: In this License Agreement:
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Applications - the software application RTG Core for genomic data
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analysis, which are made available by RTG on the site
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www.realtimegenomics.com, including any update of those applications
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made available by RTG.
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Academic Non-Commercial Research - research that is not carried out
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for profit or for commercial use. It includes:
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* sponsored academic research;
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* use of the Applications as part of a pipeline analysing data owned
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by third parties and provision of the results to those third
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parties, provided the User is not carrying out a commercial
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service and the results are not intended for commercial use.
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Documentation - any user and technical documentation made available by
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RTG on the site www.realtimegenomics.com and designed to enable the
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understanding, use and operation of the Applications or Source Code,
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including any update of that documentation made available by RTG.
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Intellectual Property Rights - includes copyright, and all rights
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conferred under statute, common law or equity in relation to
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inventions (including patents), registered and unregistered trade
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marks and designs, circuit layouts, data and databases, confidential
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information, know-how, and all other rights resulting from
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intellectual activity. Intellectual Property has a consistent
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meaning.
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Purpose - the approved purpose set out in clause 2.2.
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RTG - Real Time Genomics Ltd.
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Source Code - the source code for the Applications made available by
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RTG on the site github.com, including any update of that source code
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made available by RTG.
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User - a person or institution using the Applications, Source Code or
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Documentation.
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2. ACCEPTANCE AND PURPOSE
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2.1. Acceptance: This License Agreement sets out the terms on which
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the User may download and use the Applications, the Source Code and
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the Documentation. On downloading, using and/or continuing to use the
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Applications, Source Code or Documentation you accept the terms of
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this License Agreement and any amendments to these terms that may be
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made from time to time by RTG.
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2.2. Purpose: This License Agreement permits use of the Applications,
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Source Code and Documentation for Academic Non-Commercial Research
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only. If you wish to use the Applications, Source Code or
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Documentation for any other purpose, you will need to purchase a
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Commercial License from RTG available via email
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[email protected] or website www.realtimegenomics.com
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3. LICENSE
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3.1. Grant of license: RTG grants to the User a royalty-free,
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non-exclusive, non-transferable and non-sublicensable license to
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download and use the Applications, Source Code and Documentation for
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the Purpose, on the terms and conditions of this License Agreement.
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4. ACCESS CONDITIONS
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4.1. Permitted use: The User may use, copy and modify all or any part
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of the Applications, Source Code and Documentation but may not sell,
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commercially exploit, distribute or sublicense the Applications,
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Source Code or Documentation or copies or modifications of them.
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4.2. Conditions: The User must:
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a. use the Applications, Source Code and Documentation for lawful
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purposes only;
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b. ensure the Applications, Source Code and Documentation are
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protected at all times from unauthorized use or disclosure;
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c. maintain all proprietary notices on the Applications, Source Code
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and Documentation;
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d. not transfer, assign, sublicense or otherwise deal with or grant a
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security interest in the Applications, Source Code or Documentation or
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the User’s rights under this License Agreement;
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e. not challenge RTG’s ownership of, or Intellectual Property Rights
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in (including patent rights), the Applications, Source Code or
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Documentation;
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f. not copy or adapt the Applications, Source Code or Documentation so
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as to circumvent the need to obtain a license;
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g. not make any representation or warranty about the Applications,
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Source Code or Documentation to any third party;
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h. notify RTG in writing immediately on it becoming aware of any
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suspected unauthorized knowledge, possession or use of the
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Applications, Source Code or Documentation; and
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i. notify RTG in writing immediately on it becoming aware of any
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allegation by a third party that the Applications, Source Code or
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Documentation infringe any rights of that third party.
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4.3. Grant back: The User grants RTG a royalty-free, non-exclusive,
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perpetual, irrevocable, world-wide licence to use in any way
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whatsoever (including using, copying, modifying, selling, commercially
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exploiting, distributing or sublicensing) any modifications of the
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Applications, Source Code or Documentation made by the User.
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5. PUBLICATION
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5.1. Publication: The User may publish the results of any research
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obtained using the Applications in accordance with this License
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Agreement, provided any publication includes an attribution to the
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effect that:
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This research was carried out using RTG Core under an Academic
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Non-Commercial License granted by Real Time Genomics Ltd.
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6. INTELLECTUAL PROPERTY
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1. Ownership: RTG (or its licensors) owns all Intellectual Property
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Rights in the Applications, Source Code and Documentation.
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7. WARRANTIES
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7.1. NO IMPLIED WARRANTIES: RTG PROVIDES THE APPLICATIONS, SOURCE CODE
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AND DOCUMENTATION ON AN AS IS BASIS. ANY IMPLIED GUARANTEE, CONDITION
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OR WARRANTY INCLUDING THOSE AS TO THEIR NON-INFRINGEMENT OF THIRD
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PARTY RIGHTS, QUALITY, FITNESS FOR PURPOSE, ACCURACY OR OPERABILITY IS
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EXCLUDED TO THE MAXIMUM EXTENT PERMITTED BY LAW.
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8. LIABILITY
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8.1. UNRECOVERABLE LOSS: RTG WILL NOT BE LIABLE TO ANY USER FOR ANY
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DIRECT, INDIRECT, CONSEQUENTIAL OR INCIDENTAL LOSS OR DAMAGE ARISING
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UNDER OR IN CONNECTION WITH THIS LICENSE AGREEMENT OR THE
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APPLICATIONS, SOURCE CODE OR DOCUMENTATION.
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8.2. MAXIMUM LIABILITY: IN ANY CIRCUMSTANCES WHERE RTG IS HELD LIABLE
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UNDER OR IN CONNECTION WITH THIS LICENSE AGREEMENT, OR IN RESPECT OF
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THE APPLICATIONS, SOURCE CODE OR DOCUMENTATION, WHETHER IN CONTRACT,
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TORT (INCLUDING FOR NEGLIGENCE), BREACH OF STATUTORY DUTY OR
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OTHERWISE, THE MAXIMUM AGGREGATE LIABILITY OF RTG TO ANY PERSON WILL
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NOT EXCEED US$50.
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8.3. Indemnity: The User indemnifies RTG against all claims, loss,
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damages, liabilities and costs (including, without limit, legal costs
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on a solicitor and own client basis) that RTG suffers or incurs as a
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result of the User breaching any term of this License Agreement or of
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the User downloading or using the Applications, Source Code or
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Documentation.
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8.4. Employees, etc: The User remains responsible for any actions of
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its personnel including its employees, students or other research
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staff. Any act or omission by the User’s personnel will be deemed to
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be a breach of this License Agreement if that act or omission, if
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carried out directly by the User, would have been a breach of this
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License Agreement.
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9. TERMINATION
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9.1. Termination rights:
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a. This License Agreement terminates automatically on the User
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breaching any of these terms.
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b. RTG may terminate this License Agreement in respect of any or all
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of the Applications, Source Code or Documentation by giving notice to
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the User or by way of providing notice on the www.realtimegenomics.com
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to that effect.
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9.2. Consequences of termination: On termination for any reason, the
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User must return to RTG or destroy all copies of the Applications,
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Source Code and Documentation in its possession or control.
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9.3. Obligations continuing: Clauses 4.3, 5, 6, 8, 9.2 and 9.3 and any
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other clauses which expressly or by implication survive termination
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continue after termination of this License Agreement for any reason.
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10. GENERAL
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10.1. Waiver: To waive a right under this License Agreement, that
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waiver must be in writing and signed by the waiving party.
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10.2. Relationship: No relationship (e.g. contractor, employment,
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joint venture, agency, trust or partnership) between RTG and the User,
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other than the limited licensor/licensee relationship expressly set
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out in these terms, exists under this License Agreement.
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10.3. Severability: Any illegality, unenforceability or invalidity of
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any provision or severable part of any provision of this License
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Agreement does not affect the legality, enforceability or validity of
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the remaining provision or provisions of this License Agreement.
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10.4. Notices: Any notices to be given to RTG under this License
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Agreement may be made by sending an email to
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[email protected].
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10.5. Variation: Any variation to this License Agreement, other than
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that made by RTG by way of update on www.realtimegenomics.com and/or
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github.com, must be in writing and signed by both parties.
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10.6. Entire agreement: This License Agreement sets out everything
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agreed by the parties relating to its subject matter and supersedes
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and cancels anything discussed, exchanged or agreed prior to its
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start.
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10.7. Assignment: RTG may assign, transfer or sublicense any of its
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rights or obligations under this License Agreement without consent
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from any User.
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10.8. Law: This License Agreement is governed by, and must be
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interpreted in accordance with, the laws of the State of California,
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without regard to conflicts of law principles. Each party submits to
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the non-exclusive jurisdiction of the Courts of the State of
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California in relation to any dispute connected with this License
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Agreement. The parties agree that the Convention for the
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International Sale of Goods does not apply.
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‎README.md

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# RTG Core Non-commercial
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Copyright (c) 2014 Real Time Genomics Ltd
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This software is provided under the Real Time Genomics Ltd Software Licence Agreement for Academic Non-commercial Research Purposes only. See [LICENSE.txt](LICENSE.txt)
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If you require a license for commercial use or wish to purchase commercial support contact us via [email protected].
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---
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## Prerequisites
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* Java 1.7 or later
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* apache ant 1.9 or later
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* ant-contrib.
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## Compile / run unit tests
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$ ant runalltests
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## Building RTG Core
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To build the RTG Core Non-Commercial package which can be locally installed and run:
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$ ant zip-nojre
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This will create an installation zip file under 'dist'.
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## Installation
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Unzip the installation zip file in your installation location and follow the instructions contained in the README.txt. This build will use the system Java by default, so ensure it is Java 1.7 or later.
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## Release history
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See [doc/ReleaseNotes.txt](doc/ReleaseNotes.txt) for release history details.
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## Support
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While some email support will be available which we will do our best to fulfill, if you have support or service requirements, talk to us about our support offerings which include guaranteed response times, training, project advice, priority bug fixes and feature requests.
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