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Installation

Choose the recommended option for your computer. Every GUI and desktop route starts from coordinate-sorted BAM/BAI files and matching peak BED files.

Computer Recommended installation
Windows 10/11 x64 Desktop app
Mac with Apple silicon Desktop app
Intel Mac or Linux Python package

Desktop app

Download the app for your computer, then open it. fp-tools opens in its own application window; no browser or Python installation is required.

Download for Windows Download for Apple silicon

Windows may ask you to confirm the unsigned preview download. For the unsigned Mac preview, drag fp-tools.app to Applications and run this once in Terminal:

xattr -dr com.apple.quarantine /Applications/fp-tools.app && open /Applications/fp-tools.app

Use this command only for fp-tools downloaded from the official OncologyLab GitHub release page.

Optional de novo motif discovery prepares its external tools on first use.

Python package

Use Python 3.11–3.13:

python -m pip install --upgrade --pre fp-tools-bio
fp-tools-gui

The Python-package GUI normally opens in your browser. If it does not, open http://127.0.0.1:8891.

On Windows, use py instead of python if needed.

Running on a remote Linux server

fp-tools-gui --host 0.0.0.0 --port 8891 --no-browser

Open http://SERVER_IP:8891 from your computer, replacing SERVER_IP with the server address. The port must be permitted by the server firewall.

Optional Docker installation

Docker provides the same complete command-line and GUI environment:

docker build -t fp-tools:latest https://github.com/oncologylab/fp-tools.git#main
docker run --rm -p 8891:8891 -v "${PWD}:/work" fp-tools:latest

Open http://127.0.0.1:8891. Your current folder is available as /work.

The Linux container also supports FASTQ-to-BAM preparation with prepare-atac; native Windows and macOS installations do not.

Optional FASTQ-to-BAM preparation

The footprinting workflows start from BAM/BAI and peak BED files. Linux users who need read preprocessing can run prepare-atac separately before starting the bulk workflow.

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