Caleydo Vials

Vials visualizes alternative splicing based on mRNAseq data. You can try out vials at http://vials.io/.

Vials uses Caleydo Web as the underlying visualization framework. This repository contains the client-side Caleydo Web plugin.

Running Vials

Note: We are currently working on a Docker based build ot simplify the deployment process. In the meanwhile create the dev environment

Pre-conditions:

Dev-Environment:

install vagrant and virtualbox and follow instructions: https://github.com/Caleydo/caleydo_web_container:
- git clone https://github.com/Caleydo/caleydo_web_container
- cd caleydo_web_container
- vagrant up - start the vagrant machine (might take a while - get a coffee :))
- vagrant ssh - login to the vagrant box
within vagrant use the caleydo manager tool to install vials and all dependencies:
- ./manage.sh clone https://github.com/Caleydo/vials
- ./manage.sh clone https://github.com/Caleydo/vials_server
- ./manage.sh resolve
within vagrant create the data structure for the demo application:
- mkdir _data
- cd _data
- mkdir vials_projects
- cd vials_projects
- download & unzip bodymap data: https://www.dropbox.com/s/xrbs250tjafjvpd/bodymap.vials_project.zip?dl=0
- cd ..
- download & unzip ref_genomes: https://www.dropbox.com/s/zoqnihdrhony4bh/reference_genomes.zip?dl=0
- resulting folder structure (excerpt):

/vagrant (or ‘caleydo_web_container’)
	_data
		reference_genomes
      hg19_broad
    vials_projects
      bodymap.vials_project
  plugins
    vials
    vials_server
    … (many others)
	….

start server:
- cd /vagrant
- ./manage server

Running vials

Access it using your web browser: http://localhost:9000/vials/

Questions ?