https://github.com/beyondpie/bioscala

Scala library for Biology
https://github.com/beyondpie/bioscala

Last synced: 5 months ago
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Scala library for Biology

• Host: GitHub
• URL: https://github.com/beyondpie/bioscala
• Owner: beyondpie
• License: gpl-3.0
• Created: 2025-04-18T19:41:29.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2025-10-18T02:27:01.000Z (8 months ago)
• Last Synced: 2025-10-19T01:42:35.486Z (8 months ago)
• Language: Scala
• Size: 925 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.org
  • License: LICENSE

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README

          
# bioscala

Scala library for Bioinformatics. Right now it's an experimental version.

** Installation

   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=.