Create proper JAR for FASTQC?

[bbimber]

Hello -

FastqQC is a very useful tool we've used for years. I know you have the ZIP version to distribute the code and dependencies; however, it would be helpful on our side if FASTQ could be built as a proper JAR that included all dependencies (especially since some are quite old, like the sam JAR. If I took a stab at writing a PR to use gradle or some similar build FASTQ, would you consider incorporating it?

[s-andrews]

We wouldn't be able to distribute the whole app as a jar since it includes things like platform specific executables and user editable configuration files and templates. The nearest you'd be able to get would be putting the java code into a single jar rather than having separately bundled class files. Even then, there are files like R templates which are inside the class structure which would be more difficult to deal with if bundled inside a single jar file.

If you want to fork the current code and create a build script which put everything into a single jar then that should be pretty easy to maintain since nothing is likely to change within the structure of the program, however it's unlikely we'll change the structure for the way the main application is distributed.

Incidentally, the last release moved the old sam.jar over to the latest htsjdk library instead if that was something which was causing you issues.