Hi I have downloaded trimmomatic version 0.39. I am trying to use it using module load trimmomatic. The problem is each time I get an error message: Unable to locate a modulefile for 'Trimmomatic-0.39/' This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable. How to fix this issue. I am using it on hpc cluster.
As far as I can see you have two options:
1) use your local install: install the jar files somewhere in one of your folders (/home ? ) and then call it directly with something like the following
java -jar <trimmomatic jar file > , which should include the path to the jar file and the jar file name. While I'm al pro those module systems you don't have to use them, you can still install and use locally installed tools
2) assuming you are not an admin on the HPC you are using: send a request to the admins to have trimmomatic installed and added to the module system (these are things a 'normal' user is not allowed to do so you have to ask for admin help here)