Scala library for Biology

Scala

1. Set up env.
   • Use conda/mamba to install java. Here we use Java version 22.0.1 mamba install conda-forge::openjdk=22.0.1
   • Then use couriser to manage scala’s tools, like sbt (project manager), scala and so on. Check the installation details here: https://get-coursier.io/docs/cli-installation
2. Compile the project
   • Under the project root, we can use sbt interactive way to compile the project. sbt then compile
   • Under the project root, we can also run sbt compile in terminal.
   • [Optional] Assemble: use sbt assembly to assemble the scala codes into target directory.
3. Run
   • Under the interactive sbt, use run to run multiple main functions, it will output the multiple main functions you can run, and then you can insert the number to run the specific one.
     • I add one “AmmMain”, which can start the interactive ammonite REPL for interactive usage like Python / R REPL.
   • If you assemble the projects, you can then java -cp target/scala-verion/version.jar someMain someArgs.

TODO:

1. Use named tuple to replace most of case classes.