DEPENDENCY_LICENSES

COPYRIGHT AND LICENSE

Copyright 2018 Signature Science, LLC

This software is distributed under the BSD 3-Clause License. 

PURPOSE
These open source metagenomics workflows were constructed to analyze the biological contents of complex environmental samples.

ACKNOWLEDGMENTS
This project builds off open source work that began in the Dahak project.

-Dahak
	-github.com/dahak-metagenomics/dahak
	-Developed by the Lab for Data Intensive Biology at the University of California, Davis
	-Copyright © 2017, The Regents of the University of California
	-BSD 3-Clause License

DEPENDENCIES
The metagenomics workflows use the following tools:

-Git
	-https://git-scm.com/
	-Trademark owned by Software Freedom Conservancy (https://git-scm.com/about/trademark)
	-GNU General Public License v2
	
-Singularity
	-www.sylabs.io/docs/
	-Copyright © 2018 Singularity
	-BSD 3-Clause License

-Snakemake
	-github.com/snakemake-workflows/docs
	-Copyright © 2016 Johannes Köstert
	-MIT License

-Open Science Framework (OSF)
	-https://osf.io/
	-Copyright © 2011-2020 
	-Apache 2.0 License

-Python 3
	-www.python.org
	-Copyright © 2001-2020 Python Software Foundation
	-Python Software Foundation License, https://docs.python.org/3/license.html

-python-datrie
	-https://github.com/pytries/datrie
	-Author Mikhail Korobov
	-GNU Lesser General Public License v2.1 or later (LGPLv2+)
	
-python-psutils
	-https://github.com/giampaolo/psutil/blob/master/LICENSE
	-Copyright (c) 2009, Jay Loden, Dave Daeschler, Giampaolo Rodola
	-BSD 3-Clause License
	
-python-matplotlib
	-https://matplotlib.org/
	-Copyright 2002 - 2012 John Hunter, Darren Dale, Eric Firing, Michael Droettboom and the Matplotlib development team
	-License based on PSF https://matplotlib.org/users/license.html

-mysql-devel
	-https://dev.mysql.com/
	-Copyright © 1997, 2020, Oracle and/or its affiliates
	-Mysql information is available at https://www.mysql.com/about/legal/licensing/oem/

-postgresql-devel
	-https://www.postgresql.org/download/linux/redhat/
	-Portions Copyright © 1996-2020, The PostgreSQL Global Development Group
	-Portions Copyright © 1994, The Regents of the University of California
	-PostgreSQL License https://www.postgresql.org/about/licence/

-Squashfs-Tools
	-https://github.com/plougher/squashfs-tools
	-Copyright 2002-2019 Phillip Lougher <phillip@squashfs.org.uk>
	-GNU General Public License v2 (or later)

-Conda
	-https://conda.io/docs/
	-Copyright © 2017, Anaconda, Inc.
	-Licensed under BSD 3-Clause and terms in conda.io/docs/license.html
	
-Biocontainers
	-https://biocontainers.pro/
	-Copyright © 2019, Yasset Perez-Riverol
	-Apache 2.0 License
	

-The following are downloaded from Biocontainers and used in the current workflows:

	-Trimmomatic version 0.36--5
		-quay.io/biocontainers/trimmomatic
		-github.com/timflutre/trimmomatic
		-Developed by the Usadel Lab of RWTH Aachen University, Germany
		-GNU General Public License v3

	-FastQC version 0.11.7--p15.22.0_2
		-quay.io/biocontainers/fastqc
		-github.com/s-andrews/FastQC
		-Developed by the Bioinformatics Group at the Babraham Institute, England
		-GNU General Public License v2

	-MultiQC version 1.4--py35_0
		-quay.io/biocontainers/multiqc
		-https://multiqc.info/
		-Developed by SciLifeLab National Genomics Infrastructure in Stockholm, Sweden
		-GNU General Public License v3
		
	-Khmer version 2.1--py35_0
		-quay.io/biocontainers/khmer
		-khmer.readthedocs.io/en/v2.1.2/user/scripts.html
		-Developed by the Lab for Data Intensive Biology at the University of California, Davis
		-Copyright (c) 2010-2015, Michigan State University. Copyright (c) 2015, The Regents of the University of California, USA
		-BSD-3-Clause License
	
	-SPAdes version 3.14.0--h2d02072_0
		-quay.io/biocontainers/spades
		-cab.spbu.ru/software/spades
		-Developed by the Center for Algorithmic Biotechnology at St. Petersburg State University, Russia
		-GNU General Public License v2
 
	-MEGAHIT version 1.1.2--py35_0
		-quay.io/biocontainers/megahit
		-github.com/voutcn/megahit
		-Developed by HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong
		-GNU General Public License v3

	-QUAST version 5.0.2--py27pl526ha92aebf_0
		-quay.io/biocontainers/quast
		-quast.sourceforge.net/
		-Developed by the Center for Algorithmic Biotechnology at St. Petersburg State University, Russia
		-Copyright (c) 2015-2018 Saint Petersburg State University
		-Copyright (c) 2011-2015 Saint Petersburg Academic University
		-GNU General Public License v2

	-Mash version 2.2--h3d38be6_0
		-quay.io/biocontainers/mash
		-github.com/marbl/Mash
		-Developed for the U.S. Department of Homeland Security by the Battelle National Biodefense Institute, LLC, USA
		-Copyright © 2015, Battelle National Biodefense Institute (BNBI)
		-MIT License, and others as described in github.com/marbl/Mash/blob/master/LICENSE.txt
	
	-Sourmash version 2.1.0--py27he1b5a44_0
		-quay.io/biocontainers/sourmash
		-github.com/dib-lab/sourmash
		-Developed by the Lab for Data Intensive Biology at the University of California, Davis, USA
		-Copyright © 2016 The Regents of the University of California
		-BSD-3-Clause License

	-Kaiju version 1.6.1--pl5.22.0_0
		-quay.io/biocontainers/kaiju
		-kaiju.binf.ku.dk/
		-Developed by the University of Copenhagen, Denmark
		-Copyright (c) 2015-2020 Peter Menzel and Anders Krogh
		-GNU General Public License v3

	-Krona version 2.7--pl5.22.0_1
		-quay.io/biocontainers/krona
		-github.com/marbl/Krona
		-Developed for the U.S. Department of Homeland Security by the Battelle National Biodefense Institute, LLC, USA
		-Copyright © 2011, Battelle National Biodefense Institute (BNBI)
		-BSD 2-clause “Simplified” License
		
	-KrakenUniq version krakenuniq_0.5.8--pl526he860b03_0
		-quay.io/biocontainers/krakenuniq
		-github.com/fbreitwieser/krakenuniq
		-Developed by the Johns Hopkins School of Medicine, Baltimore, MD, USA
		-GNU General Public License v3
	
	-Kraken2 version 2.0.8_beta--pl526h6bb024c_0
		-quay.io/biocontainers/kraken2
		-ccb.jhu.edu/software/kraken2/
		-Developed by the Johns Hopkins School of Medicine, Baltimore, MD, USA
		-Copyright (c) 2017-2018 Derrick Wood
		-MIT License
	
	-Bracken version 2.2--py27h2d50403_1
		-quay.io/biocontainers/bracken
		-ccb.jhu.edu/software/bracken/
		-Developed by the Johns Hopkins School of Medicine, Baltimore, MD, USA
		-GNU General Public License v3
	
	-MTSv version 1.0.6--py36hc9558a2_1
		-quay.io/biocontainers/mtsv
		-github.com/FofanovLab/MTSv
		-Developed by the Fofanov Bioinformatics Lab at Northern Arizona University, USA
		-Copyright (c) 2018 FofanovLab
		-MIT License
		
	-SRST2 version 0.2.0--py27_2
		-quay.io/biocontainers/srst2
		-github.com/katholt/srst2
		-Developed by the University of Melbourne, Australia
		-Copyright (c) 2013, Michael Inouye, Bernie Pope, Harriet Dashnow, Kathryn Holt
		-BSD License
		
	-HUMAnN2 version 2.8.1--py27_0
		-quay.io/biocontainers/humann2
		-huttenhower.sph.harvard.edu/humann
		-Developed by the Huttenhower Lab at Harvard T.H. Chan School of Public Health, Boston, MA, USA
		-MIT License

-Docker
	-www.docker.com/legal/components-licenses
	-Copyright © 2019 Docker Inc. All rights reserved.
	-Apache 2.0 license

-The following are downloaded from Docker Hub and used in the current workflows:

	-ABRicate version 0.5-dev
		-hub.docker.com/r/thanhleviet/abricate/
		-github.com/tseemann/abricate
		-Developed by the Seemann Lab at the University of Melbourne, Australia
		-GNU General Public License v2
		
	-Prokka version 1.14.5-1
		-hub.docker.com/r/ummidock/prokka/
		-github.com/tseemann/prokka
		-Developed by the Seemann Lab at the University of Melbourne, Australia
		-GNU General Public License v3
		
-R and R Markdown
	-github.com/rstudio/rmarkdown
	-hsvn.r-project.org/R/trunk/doc/COPYRIGHTS
	-www.r-project.org/Licenses/
	-GNU General Public License v3

	-R packages used:
		-package version license
		-dplyr 0.8.4 MIT
		-tidyr 0.8.1 MIT
		-stringr 1.3.1 GPL-2
		-rjson 0.2.20 GPL-2
		-RSQLite 2.2.0 LGPL (>= 2.1)
		-remotes 2.1.1 GPL (>= 2)
		-hoardr 0.5.2 MIT
		-curl 3.2 MIT
		-DBI 1.1.0 LGPL (>= 2.1)
		-dbplyr 1.2.2 MIT
		-magrittr 1.5 MIT
		-roxygen2 7.0.2 GPL (>= 2)
		-testthat 2.3.1 MIT
		-taxizedb 0.1.9.9130 MIT
		-ggplot2 3.0.0 GPL-2
		-ggfittext 0.9.0 GPL-2
		-ellipsis 0.3.0 GPL-3
		-generics 0.0.2 GPL-2
		-glue 1.3.0 MIT
		-lifecycle 0.2.0 GPL-3
		-R6 2.3.0 MIT
		-rlang 0.4.4 GPL-3
		-tibble 2.1.3 MIT
		-tidyselect 1.0.0 GPL-3
		-vctrs 0.2.3 GPL-3
		-cli 2.0.1 MIT
		-crayon 1.3.4 MIT
		-fansi 0.4.0 GPL (>= 2)
		-pillar 1.4.3 GPL-3
		-pkgconfig 2.0.2 MIT
		-purrr 0.3.3 GPL-3
		-digest 0.6.17 GPL (>= 2)
		-assertthat 0.2.0 GPL-3
		-utf8 1.1.4 Apache License (== 2.0)
		-cpp11 0.2.3 MIT
		-stringi 1.2.4 file LICENSE
		-bit64 0.9.7 GPL-2
		-blob 1.2.1 GPL-3
		-memoise 1.1.0 MIT
		-Rcpp 1.0.3 GPL (>= 2)
		-BH 1.66.0.1 BSL-1.0
		-plogr 0.2.0 MIT
		-bit 1.1.15.2 GPL-2
		-rappdirs 0.3.1 MIT
		-brew 1.0.6 GPL-2
		-commonmark 1.7 BSD_2_clause
		-desc 1.2.0 MIT
		-knitr 1.2 GPL
		-pkgload 1.0.2 GPL-3
		-xml2 1.2.5 GPL (>= 2)
		-rprojroot 1.3.2 GPL-3
		-evaluate 0.12 MIT
		-highr 0.7 GPL
		-markdown 0.8 GPL-2
		-yaml 2.2.0 BSD_3_clause
		-xfun 0.3 MIT
		-pkgbuild 1.0.6 GPL-3
		-rstudioapi 0.8 MIT
		-withr 2.1.2 GPL (>= 2)
		-mime 0.6 GPL
		-callr 3.4.2 MIT
		-prettyunits 1.1.1 MIT
		-backports 1.1.2 GPL-2
		-processx 3.4.2 MIT
		-ps 1.3.2 BSD_3_clause
		-praise 1.0.0 MIT
		-readr 1.1.1 GPL (>= 2)
		-clipr 0.4.1 GPL-3
		-hms 0.4.2 GPL-3
		-gtable 0.2.0 GPL-2
		-isoband 0.2.2 MIT
		-MASS 7.3.51.4 GPL-2 | GPL-3
		-mgcv 1.8.28 GPL (>= 2)
		-scales 1.0.0 MIT
		-nlme 3.1.139 GPL (>= 2)
		-Matrix 1.2.17 GPL (>= 2)
		-farver 2.0.3 MIT
		-labeling 0.3 MIT
		-munsell 0.5.0 MIT
		-RColorBrewer 1.1.2 Apache License 2.0
		-viridisLite 0.3.0 MIT
		-lattice 0.20.38 GPL (>= 2)
		-colorspace 1.3.2 BSD_3_clause
		-shades 1.4.0 BSD_3_clause