Vidjil: open-source and licenses

Vidjil is open-source, released under GNU GPLv3+ license. You are welcome to redistribute it under certain conditions. This software is for research use only and comes with no warranty.

The development code is available on http://gitlab.vidjil.org/. Bug reports, issues and patches are welcome.

Licenses for third-party software and databases

Vidjil provide ready-to-use docker containers for a full client/server web application. See instructions on http://www.vidjil.org/doc/server/#docker-installation. The containers include third-party software and libraries under open-source licenses.

Moreover, they allow to download and use germline sequences and other sequences originating from both NCBI and IMGT/GENE-DB. For this, you should in particular comply to IMGT conditions (free for academic and non-profit usage).

vidjil-algo

Software and libraries included in Vidjil repository

CLI11 : Command line parser for C++11 * @version 1.7.1 * @author Henry Schreiner, Philip Top, and collaborators * @link https://github.com/CLIUtils/CLI11 * @license BSD

gzstream : iostream classes wrapping the zlib compression library * @version 1.7 * @author Deepak Bandyopadhyay, Lutz Kettner * @link http://www.cs.unc.edu/Research/compgeom/gzstream/ * @license LGPL

json : JSON for Modern C++ * @version 3.9.1 * @author Niels Lohmann * @link https://github.com/nlohmann/json * @license MIT

unbam (htslib) : Extract of htslib to only read BAM files * @version ?? * @link http://www.htslib.org/ * @license Modified BSD

vidjil-client

Software and libraries included in Vidjil repository

bioseq.js : fast and lightweight javascript library for affine-gap local and banded global pairwise alignment (Smith-Waterman) * @version d8adcf1 (2019-08-08) * @author Heng Li (lh3) * @link https://github.com/lh3/bioseq-js * @license MIT

d3-v3 : framework svg * @version 5.14.1 (2019) * @author Michael Bostock * @link http://d3js.org/ * @license BSD

jQuery : fast, small, and feature-rich JavaScript library * @version 3.3.1 (2018-01-20) * @author John Resig and jQuery team * @link http://jquery.org * @license MIT * @compatibility IE 9+, Chrome (x-1)+, Firefox (x-1)+, Safari (x-1)+, Opera x+ x is "current version" at time of release => 2.1.1: => 3.x:

file.js : load/save cross-navigator * @version (<= 2014) * @author Eli Grey * @link http://eligrey.com * @license MIT

jstree : distant file explorator * @version 3.3.3 (2016-10-31) * @author Ivan Bozhanov * @link https://www.jstree.com/ * @license MIT

less : dynamic stylesheet * @version less-1.5.0 * @author Alexis Sellier * @link self@cloudhead.net / http://lesscss.org/ * @license Apache v2

qunit.js : Unit testing * @version 2.9.1 (2019-01-07) * @author QUnit team (Trent Willis et al) * @link http://qunitjs.com/ * @license MIT

qunit-tap.js : TAP Output Producer Plugin for QUnit * @version 1.5.1 (2016-06-20) * @author Takuto Wada * @link https://github.com/twada/qunit-tap * @license MIT/GPLv2

require.js : JavaScript file and module loader * @version 2.3.6 (2018-08-27) * @author The Dojo Foundation All Rights Reserved. * @link http://jrburke.com / http://requirejs.org/ * @license MIT * @compatibility IE 6+, Firefox 2+, Safari 3.2+, Chrome 3+, Opera 10+

svgExport.js : Export SVG to PNG * @author Nikita Rokotyan, adapted by the Vidjil Team * @version retrieven on 2018-09-14 * @link http://bl.ocks.org/Rokotyan/0556f8facbaf344507cdc45dc3622177 * @license MIT

tsne.js : Implementation of TSNE algorithm * @version 2d62a1c4 (2015-10-13) * @author Andrej Karpathy * @link https://github.com/karpathy/tsnejs * @license MIT

Base docker image

nginx:1.15.0 : docker image used as base for vidjil-client docker image * @license BSD

Additional packages installed in the image

wget * @license GPLv3 * @link https://www.gnu.org/software/wget/

make * @license GPLv3 * @link https://www.gnu.org/software/make/

unzip * @license BSD like * @link ftp://ftp.info-zip.org/pub/infozip/UnZip.html

git * @license GPLv2 * @link https://git-scm.com/about

curl * @license MIT/X like * @link https://curl.se/docs/copyright.html

fcgiwrap * @license MIT * @link https://github.com/gnosek/fcgiwrap

vidjil-server

Software and libraries included in Vidjil repository

web2py : python CMS * @author Massimo Di Pierro & al * @link http://www.web2py.com/init/default/license * @license LGPLv3

Base docker image

ubuntu 18.04 : docker image used as base for vidjil-server docker image * @license https://ubuntu.com/licensing

Additional packages installed in the image

wget * @license GPLv3 * @link https://www.gnu.org/software/wget/

make * @license GPLv3 * @link https://www.gnu.org/software/make/

unzip * @license BSD like * @link ftp://ftp.info-zip.org/pub/infozip/UnZip.html

git * @license GPLv2 * @link https://git-scm.com/about

curl * @license MIT/X like * @link https://curl.se/docs/copyright.html

fcgiwrap * @license MIT * @link https://github.com/gnosek/fcgiwrap

cron * @license GPLv2+ * @link http://changelogs.ubuntu.com/changelogs/pool/main/c/cron/cron_3.0pl1-136ubuntu2/copyright

python * @license open/GPL compatible * @link https://docs.python.org/3/license.html

ipython * @license BSD3 * @link https://github.com/ipython/ipython/blob/master/LICENSE

python-cffi * @license MIT * @link https://pypi.org/project/cffi/

python-ijson * @license BSD * @link https://pypi.org/project/ijson/

python-enum34 * @license BSD * @link https://pypi.org/project/enum34/

python-requests * @license Apache License 2.0 * @link https://pypi.org/project/requests/

gosu * @license Apache License 2.0 * @link https://github.com/tianon/gosu/blob/master/LICENSE

libyajl2 * @license ISC * @link https://metadata.ftp-master.debian.org/changelogs//main/y/yajl/yajl_2.1.0-2_copyright

gnupg * @license GPLv3 * @link https://gnupg.org/

apt-utils * @license GPLv2+ * @link https://packages.ubuntu.com/bionic/apt-utils

pyuwsgi * @license GPLv2 * @link https://pypi.org/project/pyuwsgi/

Germline/sequence databases

Both vidjil-algo and vidjil-client may use sequences from any germline database. We provide tools to download these sequences in the germline/ directory. You should ensure that you comply with the provisions of the databases you download and use.

NCBI * @license NCBI itself places no restrictions on the use or distribution of the data contained therein. However NCBI cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in the molecular databases. * @link https://www.ncbi.nlm.nih.gov/home/about/policies/

IMGT/GENE-DB * @license CC BY-NC-ND 4.0 for academic users and not-profit organizations * @link http://www.imgt.org/about/termsofuse.php#conditions