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yo phovea:migrate
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‎.editorconfig

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# EditorConfig helps developers define and maintain consistent
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# coding styles between different editors and IDEs
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# editorconfig.org
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root = true
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[*]
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# Change these settings to your own preference
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indent_style = space
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indent_size = 2
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# We recommend you to keep these unchanged
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end_of_line = lf
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charset = utf-8
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trim_trailing_whitespace = true
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insert_final_newline = true
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[*.md]
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trim_trailing_whitespace = false

‎.gitattributes

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*.less text
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*.styl text
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*.js text
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*.ts text
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*.coffee text
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*.json text
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*.htm text

‎.gitignore

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style.css
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/*.map
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pileup ENSG00000149557.json
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pileup ENSG00000150782.json
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response_tp53_v3.json
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data
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/.tscache
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/.idea
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/build/
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/dist/
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node_modules/
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/src/**/*.js
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/tests/**/*.js
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*.map
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*.css
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*.log

‎.travis.yml

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language: node_js
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node_js:
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- 6
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before_install:
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- export DISPLAY=:99.0
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- sh -e /etc/init.d/xvfb start
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- if [[ `npm -v` != 3* ]]; then npm i -g npm@3; fi
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script: npm run dist
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deploy:
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provider: releases
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api_key:
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secure: 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file: dist/vials.tar.gz
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on:
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tags: true
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notifications:
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slack:
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secure: 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on_success: change
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on_failure: change

‎.yo-rc.json

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{
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"generator-phovea": {
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"type": "app",
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"name": "vials",
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"author": "The Caleydo Team",
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"githubAccount": "phovea",
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"modules": [
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"phovea_d3",
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"phovea_core"
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],
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"extensions": [
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{
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"type": "datatype",
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"id": "caleydo-genome-data-link",
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"module": "caleydo-genome-data-link",
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"extras": {}
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},
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{
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"type": "vis",
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"id": "vials-isoforms",
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"module": "vials-isoforms",
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"extras": {
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"name": "Alternative Splicing - IsoForms",
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"size": [
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840,
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300
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],
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"filter": "caleydo-genome-data-link"
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}
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},
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{
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"type": "vis",
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"id": "vials-junctions",
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"module": "vials-junctions-v2",
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"extras": {
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"name": "Alternative Splicing - Junctions",
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"size": [
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840,
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2000
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],
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"filter": "caleydo-genome-data-link"
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}
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},
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{
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"type": "vis",
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"id": "vials-reads",
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"module": "vials-read-v2",
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"extras": {
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"name": "Alternative Splicing - Read Abundance",
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"size": [
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840,
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2000
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],
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"filter": "caleydo-genome-data-link"
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}
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},
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{
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"type": "vis",
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"id": "vials-axis",
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"module": "vials-genome-axis",
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"extras": {
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"name": "Alternative Splicing - Axis",
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"size": [
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840,
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2000
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],
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"filter": "caleydo-genome-data-link"
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}
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},
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{
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"type": "app",
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"id": "vials",
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"module": "",
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"extras": {
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"name": "Vials"
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}
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}
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],
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"sextensions": [],
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"libraries": [
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"d3",
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"bootstrap",
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"font-awesome",
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"jquery"
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],
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"unknown": {
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"requirements": [],
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"debianPackages": [],
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"redhatPackages": []
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},
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"app": "",
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"entries": {
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"app": "./src/index.ts"
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},
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"libraryAliases": {
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"d3": "d3/d3"
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},
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"libraryExternals": [
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"d3",
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"bootstrap",
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"bootstrap-sass",
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"font-awesome",
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"jquery",
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"d3"
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],
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"ignores": [],
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"today": "Tue, 08 Nov 2016 12:13:12 GMT"
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}
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}

‎LICENSE

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Copyright (c) 2014, The Caleydo Team
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Copyright (c) 2016, The Caleydo Team
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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Redistribution and use in source and binary forms, with or without modification,
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are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
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* Neither the name of the {organization} nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Neither the name of the Caleydo Software nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
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ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README.md

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Caleydo Vials ![Caleydo Web Application](https://img.shields.io/badge/Caleydo%20Web-Application-1BA64E.svg)
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===================
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vials [![Phovea][phovea-image]][phovea-url] [![NPM version][npm-image]][npm-url] [![Build Status][travis-image]][travis-url] [![Dependency Status][daviddm-image]][daviddm-url]
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=====================
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Vials visualizes alternative splicing based on mRNAseq data. You can try out vials at http://vials.io/.
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Installation
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------------
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*Note:* We are currently working on a Docker based build ot simplify the deployment process. In the meanwhile create the development environment as described in following.
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[Set up a virtual machine using Vagrant](http://www.caleydo.org/documentation/vagrant/) and run these commands inside the virtual machine:
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```bash
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./manage.sh clone Caleydo/vials
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./manage.sh clone Caleydo/vials_server
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./manage.sh resolve
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```
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Within vagrant create the data structure for the demo application:
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- `mkdir _data`
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- `cd _data`
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- `mkdir vials_projects`
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- `cd vials_projects`
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- download & unzip bodymap data: https://www.dropbox.com/s/xrbs250tjafjvpd/bodymap.vials_project.zip?dl=0
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- `cd ..`
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- download & unzip ref_genomes: https://www.dropbox.com/s/zoqnihdrhony4bh/reference_genomes.zip?dl=0
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- resulting folder structure (excerpt):
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```
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/vagrant (or ‘caleydo_web_container’)
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_data
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reference_genomes
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hg19_broad
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vials_projects
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bodymap.vials_project
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plugins
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vials
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vials_server
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… (many others)
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….
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git clone https://github.com/phovea/vials.git
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cd vials
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npm install
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```
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Start server:
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- `cd /vagrant`
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- `./manage server`
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Testing
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-------
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Access it using your web browser: http://localhost:9000/vials/
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```
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npm run test
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```
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Building
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--------
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Contact
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------------
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```
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npm run build
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```
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Get in touch with us: @HendrikStrobelt or @sgratzl .
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***
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<a href="https://caleydo.org"><img src="http://caleydo.org/assets/images/logos/caleydo.svg" align="left" width="200px" hspace="10" vspace="6"></a>
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This repository is part of **[Caleydo Web](http://caleydo.org/)**, a platform for developing web-based visualization applications. For tutorials, API docs, and more information about the build and deployment process, see the [documentation page](http://caleydo.org/documentation/).
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This repository is part of **[Phovea](http://phovea.caleydo.org/)**, a platform for developing web-based visualization applications. For tutorials, API docs, and more information about the build and deployment process, see the [documentation page](http://caleydo.org/documentation/).
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[phovea-image]: https://img.shields.io/badge/Phovea-Application-1BA64E.svg
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[phovea-url]: https://phovea.caleydo.org
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[npm-image]: https://badge.fury.io/js/vials.svg
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[npm-url]: https://npmjs.org/package/vials
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[travis-image]: https://travis-ci.org/phovea/vials.svg?branch=master
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[travis-url]: https://travis-ci.org/phovea/vials
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[daviddm-image]: https://david-dm.org/phovea/vials.svg?theme=shields.io
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[daviddm-url]: https://david-dm.org/phovea/vials

‎karma.conf.js

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/* *****************************************************************************
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* Caleydo - Visualization for Molecular Biology - http://caleydo.org
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* Copyright (c) The Caleydo Team. All rights reserved.
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* Licensed under the new BSD license, available at http://caleydo.org/license
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**************************************************************************** */
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const webpack = require('./webpack.config.js');
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module.exports = (config) => {
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config.set({
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// frameworks to use
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// available frameworks: https://npmjs.org/browse/keyword/karma-adapter
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frameworks: ['jasmine'],
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// list of files / patterns to load in the browser
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files: [
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'tests.webpack.js' //just load this file
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],
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// preprocess matching files before serving them to the browser
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// available preprocessors: https://npmjs.org/browse/keyword/karma-preprocessor
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preprocessors: {
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// add webpack as preprocessor
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'tests.webpack.js': ['webpack', 'sourcemap']
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},
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webpack: webpack('test'),
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failOnEmptyTestSuite: false,
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// test results reporter to use
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// possible values: 'dots', 'progress'
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// available reporters: https://npmjs.org/browse/keyword/karma-reporter
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reporters: ['progress'],
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// enable / disable watching file and executing tests whenever any file changes
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autoWatch: false,
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// middleware: ['polyfill'],
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// BUG that install everything "karma-polyfill-service": "github:sgratzl/karma-polyfill-service",
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polyfill: {
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// features: '<feature-set>', // feature set, see polyfill-service docs for details, defaults to `{default: {}}`
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// path: '<path>' // path to serve the polyfill script under, defaults to '/polyfill.js'
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},
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browsers: [process.env.CONTINUOUS_INTEGRATION ? 'Firefox' : 'Chrome'],
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// Continuous Integration mode
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// if true, Karma captures browsers, runs the tests and exits
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singleRun: true
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});
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};

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