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.