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mkdocs.yml

@@ -5,6 +5,8 @@ docs_dir: rtd
 pages:
     - Introduction: 'index.md'
     - User Guide:
-        - 'Installation': 'user-guide/installation.md'
-        - 'Output files': 'user-guide/output-files.md'
-    - 'License': 'license.md'
+        - Installation: 'user-guide/installation.md'
+        - Output files: 'user-guide/output-files.md'
+        - Note on recalibration: 'user-guide/recal.md'
+    - License: 'license.md'
+    - Software License Agreement: 'agreement.md'

rtd/agreement.md

@@ -0,0 +1,146 @@
+SOFTWARE LICENSE AGREEMENT (hereinafter referred to as AGREEMENT)
+=================================================================
+
+This is a legal agreement between you (hereinafter referred to as the LICENSEE)
+and the University of Zurich, Rämistrasse 71, 8006 Zurich (hereinafter referred
+to as UNIVERSITY OF ZURICH) pertaining to the right to use the software product
+“MinVar” (hereinafter referred to as SOFTWARE). Using the SOFTWARE indicates
+your acceptance of these terms and conclusion of the Agreement between the
+LICENSEE and UNIVERSITY OF ZURICH.
+
+1. Introduction
+---------------
+
+1.1 UNIVERSITY OF ZURICH Institute of Medical Virology, Dr. Osvaldo Zagordi
+(PRINCIPAL INVESTIGATOR) has developed the SOFTWARE.
+
+1.2 LICENSEE wishes to obtain a non-exclusive, non-transferable and
+royalty-free license of the SOFTWARE for internal non-commercial research
+purposes as specified in this AGREEMENT.
+
+2. Grant/Scope of License
+-------------------------
+
+2.1 UNIVERSITY OF ZURICH hereby grants to LICENSEE a non-exclusive,
+non-transferable, royalty-free license to use the SOFTWARE and any related
+documentation for internal non-commercial research purposes. Commercial use of
+the SOFTWARE requires a separately executed written license agreement.
+
+2.2 UNIVERSITY OF ZURICH will not provide any services or support in connection
+with the SOFTWARE or technical support within the scope of this AGREEMENT.
+
+3. Permitted Use and Restrictions
+---------------------------------
+
+3.1 The license granted herein is for the internal non-commercial research
+purposes of LICENSEE only.
+
+3.2 LICENSEE may not duplicate or use the SOFTWARE or its contents to
+manufacture or provide products, services or technologies (or portions thereof)
+either directly or indirectly for commercialization or for any other direct or
+indirect for-profit purposes.
+
+3.3 LICENSEE agrees to reference the publication:
+
+_Huber et al._, MinVar: A rapid and versatile tool for HIV-1 drug resistance
+genotyping by deep sequencing  
+Journal of Virological Methods, Volume 240, February 2017, Pages 7-13  
+https://doi.org/10.1016/j.jviromet.2016.11.008
+
+in any publications reporting use of it or any manual or document.
+The LICENSEE is asked to forward to the PRINCIPAL INVESTIGATOR a copy of all
+reports and papers that are for public or general release that use the
+SOFTWARE.
+
+4. Warranty Disclaimer
+----------------------
+
+4.1 THE LICENSED SOFTWARE IS PROVIDED "AS IS" AND UNIVERSITY OF ZURICH MAKES NO
+REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE, BUT
+WITHOUT LIMITATION, UNIVERSITY OF ZURICH MAKES NO REPRESENTATIONS OR WARRANTIES
+OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE FUNCTIONS
+CONTAINED IN THE SOFTWARE WILL MEET LICENSEE'S REQUIREMENTS OR THAT THE USE OF
+THE LICENSED SOFTWARE OR DOCUMENTATION WILL NOT INFRINGE ANY THIRD PARTY'S
+PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. FURTHERMORE, UNIVERSITY OF
+ZURICH DOES NOT WARRANT OR MAKE ANY REPRESENTATIONS REGARDING THE USE OR THE
+RESULTS OF THE USE OF THE SOFTWARE IN TERMS OF CORRECTNESS, ACCURACY,
+RELIABILITY, OR OTHERWISE OR THAT DEFECTS IN THE SOFTWARE WILL BE CORRECTED.
+UNIVERSITY OF ZURICH WILL NOT BE LIABLE FOR ANY CONSEQUENTIAL, INCIDENTAL, OR
+SPECIAL DAMAGES, OR ANY OTHER RELIEF, OR FOR ANY CLAIM BY ANY THIRD PARTY,
+ARISING FROM THE USE OF THE LICENSED SOFTWARE.
+
+4.2 The LICENSEE expressly acknowledges and agrees that the use of the SOFTWARE
+is at LICENSEE's sole risk and to hold harmless and indemnify UNIVERSITY OF
+ZURICH, and its affiliates, employees or partners, from and against any third
+party claim arising from or in any way related to LI-CENSEE's use of SOFTWARE,
+violation of this AGREEMENT or any other actions in connection with the use of
+SOFTWARE.
+
+5. Title and Ownership
+----------------------
+
+Title, ownership rights, and intellectual property rights in and to the
+SOFTWARE shall remain with UNIVERSITY OF ZURICH.
+
+6. Term and Termination
+-----------------------
+
+6.1 This AGREEMENT shall become effective upon download of the SOFTWARE by
+LICENSEE.
+
+6.2 UNIVERSITY OF ZURICH may terminate this AGREEMENT upon 30 (thirty) days
+advance written e-mail notification to LICENSEE. Upon evidence of violation of
+any of the terms under this AGREEMENT by LICENSEE, UNIVERSITY OF ZURICH may
+terminate this AGREEMENT without previous notice.
+
+6.3 Upon termination LICENSEE is obliged to uninstall the SOFTWARE from all its
+computers and to destroy any copies of the SOFTWARE kept according to this
+AGREEMENT.
+
+6.4 Unless earlier terminated, this AGREEMENT shall automatically expire at the
+end of two years after download of the SOFTWARE by LICENSEE.
+
+6.5 Articles  4  and 5  shall survive the termination or expiration of this
+AGREEMENT for any reason in addition to those articles surviving by operation
+of law.
+
+7. Miscellaneous
+----------------
+
+7.1 This AGREEMENT and the license granted herein or any part thereof under
+this AGREEMENT are not assignable by LICENSEE without the prior written
+approval of UNIVERSITY OF ZURICH.
+
+7.2 LICENSEE shall not use the names or trademarks of UNIVERSITY OF ZURICH, its
+related entities and its employees, or any adaptations thereof, in any
+advertising, promotional or sales literature, or in any securities reports
+required by the respective authorities, without the prior written consent of
+the UNIVERSITY OF ZURICH.
+
+7.3 Each party is acting as an independent contractor and not as an agent,
+partner, or joint venture with the other party for any purpose. Neither party
+shall have any right, power or authority to act or create any obligation,
+express or implied, on behalf of the other.
+
+7.4 This AGREEMENT sets forth the entire AGREEMENT between the parties with
+respect to the subject matter hereof. No supplement, modification or amendment
+of this AGREEMENT shall be binding, unless in writing signed by a duly
+authorized representative of each party to the AGREEMENT.
+
+7.5 Should some or several provisions of this AGREEMENT be ineffective or
+invalid, or should there be an omission in this AGREEMENT, the effectiveness,
+respectively the validity of the remaining provisions shall not be affected
+thereby. An ineffective, respectively, invalid provision shall be replaced by
+the interpretation of the agreement which comes nearest to the economic meaning
+and the envisaged economic purpose of the ineffective respectively, invalid
+provision. The same applies in the case of a contractual gap
+
+7.6 The terms stipulated in this AGREEMENT may not be modified in any way
+without the mutual consent of the parties in writing.
+
+8. Governing Law and Jurisdiction
+---------------------------------
+
+THIS AGREEMENT SHALL BE GOVERNED BY THE LAWS OF SWITZERLAND. Any dispute
+arising from or in connection with this AGREEMENT will be finally settled by
+the courts of Zurich, Switzerland.

rtd/license.md

@@ -1,9 +1,33 @@
 # License
 
-MinVar relies on some third-party tools with their own specific licenses.
-It is worthy of note that recalibration is done by GATK, which is itself
+MinVar is licensed for free for non-commercial purposes according to
+[this agreement](agreement.md). Its commercial use requires a separately
+executed written license agreement, please
+[contact us](https://ozagordi.github.io/MinVar/#contact).
+
+MinVar relies on the following libraries with their own specific licenses:
+
+- pandas (library for data analysis) [simplified BSD licence](http://pandas.pydata.org/pandas-docs/stable/overview.html#license)
+- Biopython (library for biological computation), distributed under [Biopython licence](https://github.com/biopython/biopython/blob/master/LICENSE.rst)
+
+The following external tools are called by the program:
+
+- BLAST (sequence alignment), code distributed in lesser GPL
+- samtools (sequence manipulation), [MIT licence](https://github.com/samtools/samtools/blob/develop/LICENSE)
+- GATK (base quality recalibration), commercial licence (see below)
+- picard-tools (sequence manipulation), only used together with GATK, [MIT licence](https://github.com/broadinstitute/picard/blob/master/LICENSE.txt)
+- bwa (sequence alignment), [GPL v3 licence](https://github.com/lh3/bwa/blob/master/COPYING)
+- seqtk (sequence filtering), [MIT licence](https://github.com/lh3/seqtk/blob/master/LICENSE)
+- lofreq (variant calling), [MIT licence](https://github.com/CSB5/lofreq/blob/master/LICENSE)
+
+### Using recalibration in a commercial setting
+
+It is worth noting that recalibration is done by GATK, which is itself
 subject to a dual purpose [licensing](https://software.broadinstitute.org/gatk/download/licensing.php):
 free for academic non-commercial research activities, subject to a fee for commercial use.
 
-While you are free to use MinVar without restriction for research purposes, its
-commercial licensing is under definition.
+Starting from v1.2, MinVar by defaults does not recalibrate the base quality
+scores (you can evaluate the difference in this
+[Note on recalibration](user-guide/recal.md)). If you decide to use MinVar
+with recalibration for commercial purposes, you will have to obtain a licence
+for GATK from Broad Institute.

rtd/user-guide/recal.md

@@ -0,0 +1,28 @@
+# Effect of recalibration
+
+MinVar can call GATK BaseRecalibrator to adjust quality scores. Up to version
+1.1 this option was on by default, from version 1.2 this has changed.
+While GATK is free for non-commercial purposes, a licence must be acquired from
+Broad Institute (creator of GATK) if one uses it for profit.
+
+In order to support users in deciding whether to buy GATK licence or not,
+this page displays a comparison of mutations detected with and without base
+quality scores recalibration.
+
+The following scatterplots report the frequencies of amino acid mutations in the
+mixes used in the [MinVar paper](http://dx.doi.org/10.1016/j.jviromet.2016.11.008)
+both with and without recalibration performed with GATK BaseRecalibrator. The
+colours indicate whether the mutation was expected or not (_i.e._, present in
+the original virus stocks), while the shape indicates the gene where it is
+found (protease or reverse transcriptase).
+
+The names of the mixes indicate different mixing proportions of viral stocks
+and viral titers (100,000 and 10,000 copies/mL). See the paper and the file
+`viral_mixes.md` in the [data repository](https://zenodo.org/record/44921) on Zenodo.
+
+
+## Geometric mix (51.6%, 25.8%, 12.9%, 6.5%, and 3.2%)
+
+![Geometric mix: 1E4 viral load](./images/scatter_plot_mix_GEO_1E4.pdf "Geometric mix 1E4")
+
+![Geometric mix: 1E5 viral load](./images/scatter_plot_mix_GEO_1E5.pdf "Geometric mix 1E5")