WGS Extract

⚠️ Currently a WIP setup of the git repo for development

Version: v44.12 DEV - 04Jan2026 Changelog

This git repo is for development of WGS Extract, if you would just like to install it, go to https://WGSE.bio/ and follow the instructions there. The rest of this readme is for developers.

Basic Dev Workflow

You might need to install python and uv in your local environment before this works. You also might need to do uv run dev.py or python dev.py to run this flow.

• Run dev.py init to init your dev environment.
  • Windows: Works on an windows 11 machine.
  • MacOS: Works on an apple silicon mac.
  • Linux: Not tested yet, maybe works?
• Run dev.py release-cache to create a local release override cache so you don't have to redownload packages from the internet repeatedly during testing & development.
• Edit - build - run: launch with dev.py launch (or WGSExtract.*), edit in your text editor, quit and launch again, etc.
• Run unit tests: uv run pytest
• Library updating: run dev.py library (or Library.*)
• Build Release Installers: run dev.py release , see output zip files in the out/installer_builds/ folder. Use release --release-override or release -ro to use your local cache for the installer, makes things much faster for testing. Users would download those zips and run the Install* scripts they see in the root.
• Installer Status
  • Test flow: install and download a genome (bash testing), MT Haplogroup (java testing), make a microarray file
  • Windows: Manually tested on a windows 11 machine to work
  • MacOS Brew: Manually tested on an apple silicon mac with homebrew
  • MacOS MacPorts: Manually tested on a UTM vm macOS 26.2
  • Ubuntu Linux: Manually tested on a UTM arm64 vm and x86 WSL to work
  • Micromamba Linux: Tested with archlinux and openSUSE tumbleweed WSL. Needed to install system packages for python & tk manually to get the app to launch, but the installer said it was successful. We got a WSL test vm working with this, so it might work with the next manual test.

Repository Structure

Git Tracked

• installer_scripts/: Platform-specific scripts used during the (un)installation process.
• scripts/: The bash scripts side of program/.
• program/: Core Python source code for the WGSExtract application and GUI.
• base_reference/ -> becomes reference/, since program/ expects that the reference/ folder also exists but we want to .gitignore it because it has downloaded data we don't want to commit to git.
• ⁠dev/ -> handles all the non-user things like making release builds, dev init, dev util scripts, etc. dev.py is the interface for that and it has a help with ./dev.py -h
• ⁠docs/ - centralizes the docs into one spot for the most part. We also converted to markdown in a semi automated way but also is txt friendly.
• sandbox/: Experimental code and temporary development work you can ignore.
• tests/: Where unit tests live

Git Ignored

• out/: Default output directory for build artifacts, download caches, tmp dirs for tests, etc. Basically the output dir of dev actions.
• reference/: Where downloaded genomes for the program/ and such live.
• temp/: Temporary files generated during execution of program/ or scripts/.

Installed Standalone Packages

• FastQC/: The FastQC quality control tool for sequence data.
• jartools/: Java utility tools (JAR files) like GATK, Picard, and HaploGrep.
• yleaf/: Integration with the Y-Leaf tool for Y-chromosome analysis.

Links

• Docs
• Development Notes
• Release
• Changelog