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Interactive (VICE) Tool Integration in DE

Goal

This quickstart contains the complete instructions for integrating interactive (VICE) tools in DE which is mainly intended for exploratory data analysis (bioinformatic and geoinformatic) as well as the ability to run ad-hoc scripts.

Tip

What is interactive tool?

Any tool that needs to run on the web browser by opening up ports is considered as an interactive tool

For more information on Interactive tools, please refer to this extensive documentation


Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise CyVerse User Portal

Platform(s)

We will use the following CyVerse platform(s):

Platform Interface Link Platform Documentation Quick Start
Discovery Environment Web/Point-and-click Discovery Environment DE Manual Discovery Environment Guide

Get started

  • Find the Docker image of your interactive tool/software of your interest
  • Test the Docker image
  • Add the interactive tool in CyVerse Discovery Environment
  1. Find the Docker image

We will use PEA-Rstudio, an integrated R toolkit for epitranscriptome analysis for integrating as an interactive tool in DE. Fortunately, there is Docker image available for PEA on Dockerhub for integrating that as an interactive tool in DE.

Note

If there is no Docker image available for your tool of interest, then you would either find a Dockerfile which you can use to build the Docker image for your tool of interest or create one. You can get more help with either of that from here

  1. Test the Docker image locally on your computer (Optional but recommended)

This is optional but highly recommended step to confirm that the Docker image for your tool of interest is working as expected. Here is how you would test PEA with the intructions they provided in their README

2.1 Pull the image from Dockerhub

$ docker pull malab/pea:v1.1_rstudio

If you are looking for a place to pull the Docker image or run the Docker container, then you can use the free resource - Play with Docker

2.2 Sample run

Once PEA-Rstudio Docker image is pulled successfully, type the following command to start PEA

$ docker run --rm -d -p 8787:8787 malab/pea:v1.1_rstudio

Note

The username and password for Rstudio is rstudio and pea respectively

Once you can open the Rstudio, then you are ready to integrate the tool in DE

  1. Add tool in CyVerse Discovery Environment

Now that the PEA-Rstudio Docker image has been tested, it is now ready to be integrated into DE.

3.1 Log-in to CyVerse Discovery Environment and click on the “Apps” window

3.2 Click “Manage Tools” -> “Tools” -> “Add Tool” and fill the details about your Docker image

add_tool_int_1

add_tool_int_2

Procede here to create an app interface in the CyVerse Discovery Environment


Additional information, help

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