Program setup

Diachromatic requires Java 8 or higher to run. Diachromatic can be obtained from the Diachromatic GitHub page. We recommend to download the Diachromatic.jar file of the latest release on the release page of the project.

You can run the program using this command:

$ java -jar Diachromatic.jar

You should see a help message in the shell.

Building Diachromatic from source

To build the application on your own, clone the repository and create the Java app with maven:

$ git clone https://github.com/TheJacksonLaboratory/diachromatic.git
$ cd diachromatic
$ mvn package

To test whether the build process was successful, enter the following command:

$ java -jar target/Diachromatic.jar

Preparation for bowtie2

The mapping step of the diachromatic pipeline relies on bowtie2. If needed, install bowtie2 on your system. For instance, on Debian linux systems bowtie2 can be installed with the following command.

$ sudo apt-get install bowtie2

The prebuilt bowtie2 indices for human hg19 (3.5 GB) and other genome builds can be downloaded from the bowtie2 website. After downloading the correct archived file to your computer, unpack it with:

$ unzip hg19.zip

In the following pages, we will call the path to the directory where the index was unpacked /path/to/bowtie2index/. Substitute this with the actual path on your computer.