caleydo / lineup_product

[DEPRECATED] Caleydo LineUp deployment --> moved to https://github.com/datavisyn/lineup_app

Caleydo - Visualization for Molecular Biology

Caleydo is a visualization framework for molecular biology data. It is targeted at analyzing multiple heterogeneous but related tabular datasets (e.g., mRNA expression, copy number status and clinical variables), stratifications or clusters in these datasets and their relationships to biological pathways.

For user documentation please refer to the Caleydo Help. For general information and downloads based on binaries please use the Caleydo Website. This guide assumes that you want to install Caleydo from source.

Installation

Caleydo uses Java, OpenGL and the Eclipse Rich Client Platform (RCP). Things you need to install before being able to run Caleydo:

• Eclipse Kepler for RCP and RAP Developers, which you can get from the eclipse download page. Other Eclipse versions won't work.
• Install EGit in Eclipse using software updates.
• Java SDK >= 1.7

To install Caleydo use EGit within Eclipse and clone the repository. Each directory in the caleydo-dev folder corresponds to an Eclipse project. Here is a good tutorial on how to import Eclipse projects from git.

If you want to use ssh (instead of https) for communicating with github out of eclipse follow these instructions. You will have to generate a new RSA key and save it to you ~/.ssh folder. Remeber to set a passphrase for you key. This will result in a file ida_rsa and ida_rsa.pub turning up in your ssh folder. Save your public rsa key with your eclipse account folder.

When cloning the repository follow the above tutorial. Don't change the username "git" to your username!

Team

Caleydo is an academic project currently developed by members of

• Institute for Computer Graphics and Vision at Graz University of Technology, Austria
• Institute of Computer Graphics at Johannes Kepler University Linz, Austria
• Pfister Lab at the School of Engineering and Applied Sciences, Harvard University, Cambridge, USA
• Park Lab at Harvard Medical School, Boston, USA

Acknowledgements

Caleydo makes use of a range of open source tools, bioinformatics resources and pre-packages several datasets, which we gratefully acknowledge here.

Software Libraries

• Bubble Sets - A Java implementation of the visualization technique.
• CDK - The Chemistry Development Kit.
• JGrahT - A graph library.
• Jogl - Java bindings for OpenGL.
• PathVisio - loading and parsing WikiPathways.
• WordHoard - statistical utilities.

Bioinformatics Resources

• David Bioinformatics Resources - Gene ID mapping.
• KEGG - Pathways.
• WikiPathways - Pathways.

Datasets

• CCLE - BROAD Institute Cancer Cell Line Encyclopedia.
• TCGA - The Cancer Genome Atlas.

Resources

• GitHub - Hosting our source code.
• WebStorm - Free developer licenses for our web projects from JetBrains.

lineup_product's Issues

Instructions to launch with non-demo data?

• Release number or git hash: c726a94
• Web browser version and OS: chrome mac
• Environment (local or deployed): local

Continuing conversation from Slack:

chuck:

Hi: We’d like to use taggle here. This much works:

$ cd lineup_product/
$ git checkout taggle
$ npm install
$ npm run build
$ docker run -d -p 8080:80 lineup:1.0.0-20180116-224540

What we’d like now is to be able to launch a given image with data we specify… maybe pass it in via an envvar, or hit some api after it launches. (We’d prefer not to bake the data, or references to the data, into the image.) Does something like that seem feasible?
(Also… If we’ll be extending what this container does, is there an official image already in dockerhub that we should use as a base, or ok to just go ahead and push the image we build?)

marc:

you can mount your datasets as a volume in the docker container.
as an alternative, you could use taggle as a JS library (without the app) and then load your data via the API. if you have further specific questions, please write an issue and sam will get back to you.

holger:

Taggle/LineUp has no backend (= no docker container). please follow these steps:

($ npm install)
$ npm run start:lineup

An npm:install should be done by the phovea:setup-workspace. You start the Taggle/LineUp using npm run start:lineup.

---

• I'm a little confused by the statement that Taggle has no backend and no docker container... Is the idea that the container I got from npm run build just something internal, and not something I would want to build on?
• On the other hand, if I can build on it, and Marc's statement ("you can mount your datasets as a volume in the docker container") is accurate, that would fit my needs well: What path should I mount the data on? Is there documentation I should be referring to?
• Trying to folger Holger's step's didn't really work for me: (From a checkout of https://github.com/Caleydo/lineup_product.git)

$ yo phovea:setup-workspace lineup_product -b taggle
$ npm install
$ npm run start:lineup
npm ERR! missing script: start:lineup

(I've tried it on the top level, and inside lineup direction... not sure if that should make a difference?)

I'd be happy with the approach of mounting a volume with the container I already have, but if I should try a different direction let me know. (Also, let me know if my end goal doesn't make sense, or it's not something lineup should be able to do.)

Taggle product should show Taggle in the about dialog