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Vidjil: open-source and licenses

Vidjil is open-source, released under the GPL version 3 or any later version. 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-algo repository

CLI11 : Command line parser for C++11

gzstream : iostream classes wrapping the zlib compression library

json : JSON for Modern C++

unbam (htslib) : Extract of htslib to only read BAM files

vidjil-client

Software and libraries included in Vidjil-client repository

bioseq.js : fast and lightweight javascript library for affine-gap local and banded global pairwise alignment (Smith-Waterman)

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

jstree : distant file explorator

less : dynamic stylesheet

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

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+

seedrandom.js : A replacement of Math.random of javascript that allow to get fixed seed

svgExport.js : Export SVG to PNG

tsne.js : Implementation of TSNE algorithm, adapted by the Vidjil Team for randomseed

select2.js : Select2 is a jQuery-based replacement for select boxes

Client base docker image

nginx : docker image used as base for vidjil-client docker image

  • @license BSD
  • @version 1.21

Additional packages installed in the client image

wget

make

unzip

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

git

curl

fcgiwrap

vidjil-server

Software and libraries included in Vidjil-server repository

py4web : python CMS

Server base docker image

ubuntu 20.04 : docker image used as base for vidjil-server docker image

Additional packages installed in the server image

wget

make

unzip

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

git

curl

fcgiwrap

cron

python

ipython

python-cffi

python-ijson

python-enum34

python-requests

gosu

libyajl2

gnupg

apt-utils

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