Cloudgene Examples

This repository includes several examples to help you developing Cloudgene applications.

Install Cloudgene

You will need the following things properly installed on your computer.

• Java 8 or higher
• Docker (Optional)

Download the latest version from our download page using the following commands:

• mkdir cloudgene
• cd cloudgene
• curl -s install.cloudgene.io | bash

Add the executable path to your PATH variable. For example:

export PATH=~/path/to/cloudgene:$PATH

Test the installation with the following command:

cloudgene version

Now you are ready!

Download Examples

You can download the content of this repository from here or use git to clone it:

git clone https://github.com/genepi/cloudgene-examples.git

Install Examples

You can install all example at once by using the clone command and the provided examples.yaml file which contains all applications:

cd cloudgene-examples
cloudgene clone examples.yaml

You can use the ls command to see which applications were installed:

cloudgene ls

Running Examples

Or you can start the Web-Application with the server command:

cloudgene server

The webservice is available on http://localhost:8082. Please use username admin and password admin1978 to login.

You can run installed applications on the commandline with the run command followed by the application id and the parameters. For example:

cloudgene run print-text --message "Hello World"

Examples

Commands and Bash

cloudgene run print-text --message "Hello World"

cloudgene run print-text-to-file --message "Hello World"

More complex tasks using Java or Groovy

cloudgene run hello-groovy
cloudgene run hello-groovy --name Lukas

Docker

You need Docker installed on your computer to run this example. This workflow starts a Docker container containg vcf-tools and calculates the allele frequency of the provided VCF file:

cloudgene run vcf-tools --vcf vcf-file.vcf.gz