Marker Workbench

CDS/エキソン、シーケンスプライマー、CAPS設計に絞ったWindows GUI。 | A focused Windows GUI for CDS/exon, sequencing-primer, and CAPS marker workflows.

This is a source-level focused distribution of Gene Research / Sequence Workbench. Unrelated top-level UI panels are removed; this is not the full application with hidden tabs.

Features / 機能

• Design CDS/exon amplification candidates
• Design sequencing amplicons
• Generate CAPS marker candidates and export reports

Requirements / 必要条件

• Windows 10 or 11
• WSL2 Ubuntu
• Node.js 20+ on Windows
• WSL packages: Python 3, python3-venv, Primer3 and NCBI BLAST+, and netcat-openbsd
• Your own genome/BLAST database where the workflow requires one

Windows版Primer3は使用しません。Primer3を使う機能はWSL版だけをサポートします。

Install and start / 導入と起動

wsl --install -d Ubuntu
wsl -d Ubuntu -- bash -lc "sudo apt update && sudo apt install -y python3 python3-venv ncbi-blast+ primer3 netcat-openbsd"
git clone https://github.com/light-suzuki/MarkerWorkbench.git
cd MarkerWorkbench
.\start_windows.bat

The launcher installs exact frontend dependencies with npm ci, creates the backend virtual environment at ~/.sequence_workbench/venvs/bioapi in WSL, starts FastAPI on port 8000 and the UI on port 5173, then opens the browser.

初回は依存関係を導入します。backendはWSL、frontendとブラウザはWindowsで動きます。

Stop:

.\stop_windows.ps1

Register your own BLAST database / 手持ちDBの登録

Store data outside the cloned repository:

mkdir -p ~/sequence-workbench-data/blastdb
makeblastdb -in ~/sequence-workbench-data/my_genome.fa -dbtype nucl \
  -out ~/sequence-workbench-data/blastdb/my_genome

Register /home/<your-wsl-user>/sequence-workbench-data/blastdb/my_genome. Use the -out prefix, not an individual index file. Data and indexes are not included in this repository.

Optional paths / 任意設定

Copy-Item backend\bioapi\.env.wsl.example backend\bioapi\.env.wsl

Use Linux paths in .env.wsl. Windows paths such as C:\data are rejected.

Verify / 検証

npm --prefix frontend\workbench ci
npm --prefix frontend\workbench run typecheck
npm --prefix frontend\workbench run build
npm --prefix frontend\workbench audit --audit-level=moderate
.\start_windows.bat
Invoke-RestMethod http://127.0.0.1:8000/health
.\stop_windows.ps1

Troubleshooting / トラブルシュート

• Startup logs: .runtime\backend.error.log, proxy.error.log, and frontend.error.log
• Primer3: run wsl which primer3_core
• BLAST+: run wsl which blastn
• Missing DB: register the WSL makeblastdb -out prefix
• Port conflict: stop the exact process using 5173 or 8000
• Do not install or configure Windows-native Primer3

Clean removal / 完全削除

Run stop_windows.ps1, then delete the clone. To also remove the shared test environment and example data:

wsl -d Ubuntu -- bash -lc "rm -rf ~/.sequence_workbench/venvs/bioapi ~/sequence-workbench-data"

No user genome, accession, sequence, private path, credential, or result is bundled. The app does not delete user data automatically.

License and contributors

MIT License. See CONTRIBUTORS.md for project and AI-assistance credits.