Hi all.

So this is probably a somewhat basic solution but unfortunately I am stuck.

I am trying to use the Shovill assembly pipeline on some data I have using our department's computer cluster. The cluster doesn't have conda, so I have been installing the dependencies manually (which is not an issue). However, I am encountering some issues when "installing" the java programs (namely Trimmomatic and Pilon). I dont have any trouble invoking the .jar file (i.e java -jar pilon-1.23.jar) however when running ./shovill --check to confirm it can call on the dependencies I get an error that says "Could not find 'pilon' - please install it.".

I know that normally I would just add the directory to $PATH and things would be fine however I am unfamiliar with Java and I do not think I can do that... I have searched to see what the fix is for something like this is but I cannot find anything which makes me feel like I am missing something crucial and probably straightforward.

Thanks!