DeepPhe Installer
This repository (installation) holds the install4j
project files, build scripts, and shared assets used to produce the DeepPhe
desktop installer for macOS, Windows, and Linux.
It does not contain the DeepPhe application code itself. Instead, it packages
a small Java launcher and, at install time, downloads the heavy DeepPhe
components from the DeepPhe/DeepPhe-Dist
GitHub releases. The result is a single installer per platform that a
non-technical user can double-click to get a working DeepPhe environment.
DeepPhe is a natural-language-processing system that extracts a structured cancer phenotype summary from clinical notes. Learn the concepts on the DeepPhe homepage and the Release Wiki.
What this repo produces
Building the project (DeepPhe-and-Launcher.install4j) writes three installer
media files to build/deepphe-installer/. When those media are published with
build-all.sh --publish, the GitHub release assets use versioned filenames:
| Platform | File | Notes |
|---|---|---|
| macOS | DeepPhe-7.1.dmg | Disk image with DeepPhe Installer.app |
| Windows | DeepPhe_windows-7.1.exe | Signed with an Authenticode certificate |
| Linux | DeepPhe_linux-x64-7.1.sh | Self-extracting shell installer |
Each installer bundles a Java 26 runtime and the DeepPhe Launcher GUI, and knows how to fetch and configure everything else on the target machine.
The two halves of DeepPhe on disk
When a user runs the installer, it creates two directories:
<install dir>/.DeepPhe/— the program: the NLP pipeline, embedded ontology database, the visualizer, the data API, the DB creator, tool binaries, and configuration. This is managed by the installer/uninstaller.~/DeepPheDocs/— the user's data:input/reports andoutput/results. This is intentionally kept out of the program folder so it survives reinstalls and upgrades.
See Installed layout for the full tree.
How the pieces fit together
Where to go next
- Installing DeepPhe: Download DeepPhe → Install DeepPhe → Launch DeepPhe.
- Removing DeepPhe: Uninstall DeepPhe.
- Maintaining the installer: Prerequisites → Local Mac DMG test → Full build.
- Shipping a release: Release checklist → Publishing installer media → Smoke-test matrix.
- Understanding internals: Install flow and Launcher.
Signing certificates, keystores, PINs, and notarization passwords are not stored in Git. This documentation only references the names of the scripts and environment variables involved — never the credential values. See Repo layout.