This repository includes several examples to help you developing Cloudgene applications.
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!
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
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
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"
cloudgene run print-text --message "Hello World"
cloudgene run print-text-to-file --message "Hello World"
cloudgene run hello-groovy
cloudgene run hello-groovy --name Lukas
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