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Windows support

AutoAB does not run on Windows today. This is not a matter of a missing build step; several parts of the tool would need changing first. This document records exactly what, so the decision to invest is an informed one.

A code audit was run against this repository specifically to answer the question. Findings are grouped by whether they stop the tool outright.

Hard blockers

# Problem Where Fix
1 No Windows IgBLAST binaries and no way to get them; the installer is bash-only and exits on any non-Darwin/Linux platform scripts/install.sh NCBI publishes ncbi-igblast-1.22.0-x64-win64.tar.gz; add a PowerShell or Node equivalent
2 IgBLAST/BLAST executables resolved without the .exe suffix backend/utils/toolpaths.py handles this now, but it is untested on Windows Verify exe() on a real Windows box
3 npm run package:win aborts: win.icon points at static/icon.ico, which does not exist (only icon.icns is present) electron-app/package.json Add a real .ico, or a ≥256px .png for electron-builder to convert
4 Two competing build configurations. package.json has a build key, so electron-builder.yml is never read, so its NSIS block, file filters and publish settings are dead electron-app/package.json, electron-app/electron-builder.yml Delete one; keep the YAML
5 extraResources copies geneGUI/bin verbatim, so cross-building from macOS ships Mach-O binaries inside the Windows installer electron-app/package.json Make extraResources platform-conditional

Items 1-2 of the original audit (hardcoded macOS Python and R paths) and the PATH/environment handling have already been fixed in this repository; see VALIDATION.md.

Would silently degrade

Problem Where Effect
os.symlink in tree visualisation backend/pipeline_runner.py Needs Developer Mode or admin on Windows; otherwise every run produces zero tree images, reported only as a non-fatal warning
IQ-TREE detection uses which backend/scripts/build-trees-iqtree.R which does not exist in cmd.exe, so every tree silently falls back to neighbour-joining
Unquoted IQ-TREE command line backend/scripts/build-trees-iqtree.R Breaks on output paths containing spaces, which is the norm on Windows
Cancel kills the process group with a negative PID electron-app/src/main/backend-runner.ts Not supported on Windows; IgBLAST and Rscript survive cancellation, keep file handles open, and subsequent cleanup fails with PermissionError. Needs taskkill /T /F
detached: true without windowsHide electron-app/src/main/backend-runner.ts Console windows flash on every spawn
Output directory under resources/geneGUI/outs electron-app/src/main/ipc-handlers.ts Writable only for per-user installs; breaks under C:\Program Files. Should use app.getPath('userData')

Cosmetic

titleBarStyle: 'hiddenInset' is macOS-only and no titleBarOverlay is set, so a Windows window would have no minimise/maximise/close buttons, and the renderer reserves 80px of padding for macOS traffic lights. Around a dozen places derive file names with split('/').pop(), which shows the whole path when the separator is \.

Explicitly ruled out

Two things that are commonly assumed to be Windows problems here are not:

  • The geneGUI/bin/internal_data symlink. It is not tracked in git at all; it is created by the installer. IgBLAST resolves internal_data from the IGDATA environment variable (falling back to the working directory), and every call site in this repository sets IGDATA explicitly. The symlink is a convenience, not a requirement.
  • CRLF line endings in the reference data. Verified against IgBLAST 1.22.0: CRLF germline FASTAs, human_gl.aux and internal_data/*.ndm/*.pdm files all parse correctly and produce identical output.

Practical alternative

Running the tool under WSL2 with an X server, or on a Linux VM, avoids all of the above and only requires the Linux install path, which scripts/install.sh already implements (though it is likewise untested).