DEPENDENCY_LICENSES.txt

PURPOSE

MetagenomeScope is a visualization tool intended to aid in the analysis of
metagenomic assembly and scaffold graphs. It consists of a preprocessing
script (implemented in Python) and a web-based visualization interface
(implemented in JavaScript, HTML, and CSS; also referred to as the "viewer
interface").

The viewer interface code is distributed with:

-Cytoscape.js
    -http://js.cytoscape.org
    -Copyright is contained in viewer/js/cytoscape.min.js
    -Licensed under the MIT License
     (included in dependency_licenses/cytoscape.js.license)

-Cytoscape.js expand-collapse extension
    -https://github.com/iVis-at-Bilkent/cytoscape.js-expand-collapse
    -Copyright is contained in
     dependency_licenses/cytoscape.js-expand-collapse.license
    -Licensed under the MIT License
     (included in dependency_licenses/cytoscape.js.license)

-Bootstrap
    -http://getbootstrap.com
    -Copyright is contained in dependency_licenses/bootstrap.license
    -Licensed under the MIT License
     (included in dependency_licenses/bootstrap.license)

-Bootstrap Colorpicker
    -https://farbelous.github.io/bootstrap-colorpicker
    -Copyright is contained in
     dependency_licenses/bootstrap-colorpicker/license
    -Licensed under the Apache License, version 2.0
     (included in dependency_licenses/bootstrap-colorpicker/apache-license-2.0)

-RequireJS
    -https://requirejs.org/
    -Copyright is contained in dependency_licenses/requirejs.license
    -License included in dependency_licenses/requirejs.license

-Underscore.js
    -https://underscorejs.org/
    -Copyright is contained in dependency_licenses/underscore.js.license
    -License included in dependency_licenses/underscore.js.license

-jQuery
    -http://jquery.com
    -Copyright is contained in dependency_licenses/jquery.license
    -Licensed under the MIT License
     (included in dependency_licenses/jquery.license)

-Mocha
    -https://mochajs.org
    -Copyright is contained in dependency_licenses/mocha.license
    -Licensed under the MIT License
     (included in dependency_license/mocha.license)

-Chai
    -https://www.chaijs.com
    -Copyright is contained in dependency_licenses/chai.license
    -Licensed under the MIT License
     (included in dependency_license/chai.license)

The Python component of the preprocessing script requires the use of the
following tools during execution, although they are not distributed with
MetagenomeScope:

-Python 3
    -https://www.python.org
    -Licensed under the Python Software Foundation License

-Graphviz
    -http://www.graphviz.org
    -Licensed under the Eclipse Public License

-Pygraphviz
    -http://pygraphviz.github.io
    -Licensed under the BSD 3-clause License

-NumPy
    -http://www.numpy.org
    -Licensed under the BSD 3-clause License

-NetworkX
    -https://networkx.org
    -Licensed under the BSD 3-clause License

-Click
    -https://click.palletsprojects.com/en/7.x/
    -Licensed under the BSD 3-clause License

-GfaPy
    -https://github.com/ggonnella/gfapy
    -Licensed under an ISC License

-pyfastg
    -https://github.com/fedarko/pyfastg
    -Licensed under the MIT License

-Jinja
    -https://jinja.palletsprojects.com/en/2.11.x/
    -Licensed under the BSD 3-clause License

The preprocessing script code was converted from Python 2 to Python 3 using
futurize as a starting point:

-futurize
    -https://python-future.org/futurize.html
    -Licensed under the MIT License

Automatic testing, style-checking, and linting is done using the following
tools that have not been mentioned yet (none of these tools are distributed
with MetagenomeScope):

-Travis-CI
    -https://travis-ci.org/
    -Copyright (C) TRAVIS CI, GMBH

-Codecov
    -https://codecov.io/
    -Copyright (C) Codecov 2019
    -codecov-bash, the script used to upload coverage reports to Codecov
     during automatic testing, is licensed under the Apache License 2.0.
     (Code for this is available at https://github.com/codecov/codecov-bash.)

-pytest
    -https://docs.pytest.org/en/latest/
    -Licensed under the MIT License

-pytest-cov
    -https://pytest-cov.readthedocs.io/en/latest/
    -Licensed under the MIT License

-Flake8
    -http://flake8.pycqa.org/en/latest/
    -Licensed under the MIT License

-Black
    -https://black.readthedocs.io/en/stable/
    -Licensed under the MIT License

-mocha-headless-chrome
    -https://github.com/direct-adv-interfaces/mocha-headless-chrome
    -Licensed under the MIT License

-nyc
    -https://istanbul.js.org/
    -Licensed under the ISC License

-Prettier
    -https://prettier.io/
    -Licensed under the MIT License

-jshint
    -https://jshint.com/
    -Licensed under the MIT License (one file licensed under the JSON License)