Integrate Trimmomatic as an external tool

Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) is a JAVA application. It can be run on all OS, supported by UGENE: Windows, Linux and macOS; 32-bit and 64-bit. The tool has license GNU GPL v.3.

Integrate it as an external tool into UGENE:

• Add a new item "Trimmomatic" to the "External Tools" page in the Application Settings. It should have the following description:

  Trimmomatic is a flexible read trimming tool for Illumina NGS data.
  

• Specify "Version" and "Binary path" below like in other external tools descriptions.
• Put all FASTA files from the "adapters" folder of the Trimmomatic archive to a new folder "illumina". Create this folder as a subfolder of ".../data/adapters" of the UGENE package.
• Use "trimmomatic-0.36.jar" as the executable file. Add it to all external tools packages.
• On the "Select Components" page of online installers add "Trimmomatic" item to the "Full package additions (include some NGS tools)/External tools" group.
• On the "License Agreement" page add the license, see this link.