I wanted to know if trimmomatic can only be run on GNU GPL v3 or it can also be run on windows environment? I am new to bioinformatics and I have no much knowledge of basic informatics neither.... I need to trim fastq files.
Trimmomatic is a Java application, and probably can be run on windows (see, for example, this discussion at Introducing the Trimmomatic). However, you will find few (if any) help around if you encounter problems. I would advise you to use Linux, or install the Windows Subsystem for Linux, in case you are using Windows 10.
GNU GPL is not an operating system, it is a software license - by the way, Trimmomatic is licensed under the GNU GPL v3.
Unzip the whole Trimmomatic folder to a destination (e.g., desktop)
Right click on .jar file in Trimmomatic folder, under Properties --> General change the application which opens .jar to "Java SE"
Alternately, right click on the .jar and go to "open with" and select Java SE
Create a new text file in the Trimmomatic folder. Rename it run.bat (ensure the extension is .bat not .txt after save).
Open the run.bat file in a text editor like Notepad and change to the shell type command that you would use in Linux (e.g. java -jar trimmomatic-0.39.jar SE -phred33 input_file_name.fastq output_file_name.fastq MINLEN:50).
Note, if you drop the new file into the Trimmomatic folder no path is needed, just file names