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.
Note: We are currently working on a Docker based build ot simplify the deployment process. In the meanwhile create the 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
- Access it using your web browser: http://localhost:9000/vials/
- Get in touch with us: @HendrikStrobelt or @sgratzl .