End-user installation walkthrough

This is what someone installing DeepPhe actually sees. It mirrors the installer screens defined in DeepPhe-and-Launcher.install4j.

For the shorter user-facing path, see Download DeepPhe, Install DeepPhe, and Uninstall DeepPhe.

Starting the installer

Platform	How to start	Privileges
macOS	Open DeepPhe-7.1.dmg, run DeepPhe Installer.app	May prompt for admin rights
Windows	Run DeepPhe_windows-7.1.exe	Requests elevation; recommends a no-space path
Linux	Run sh DeepPhe_linux-x64-7.1.sh after downloading DeepPhe_linux-x64-7.1.sh	Standard install4j Unix installer

The wizard screens

1. Welcome — intro screen with a customized title bar.

2. Choose install directory —

   • The installer shows the required disk space.
   • On Windows, a note warns that the directory path must not contain a space (an external pipeline dependency requires this). The installer defaults to a no-space location such as C:\DeepPhe and validates the chosen path.

3. Components — select what to install.

4. Installation — a progress screen. While files download and unpack, the installer shows helpful links:

   • DeepPhe Homepage — key concepts, demos, publications.
   • DeepPhe Wiki — tutorials and how to prepare data.

   Status messages progress through: Downloading DeepPhe file packs and platform binaries… → Unpacking DeepPhe Files… → Performing Configuration Operations… → Cleaning Up Install Folder…

5. Finished — offers two links:

   • The DeepPhe User Survey — the team asks users to fill it out so they can report accurate usage numbers to their funding agency.
   • The Release Wiki for getting-started help.

This step needs internet

Because the installer downloads DeepPhe's payloads from GitHub during installation (see Install flow), the machine must have network access while installing. The downloads are ~50–110 MB each.

After installing

The installer creates the DeepPhe Launcher (with a rocket icon), a program group / Start-menu entry, and an Add/Remove Programs registration. Launch it to open the DeepPhe Desktop GUI, which starts pre-loaded with an example project pointing at the bundled example corpus. See Launcher.

Uninstalling

Run the uninstaller for the distribution that was installed:

Platform	How to uninstall	Notes
macOS	In the chosen install directory, run DeepPhe Uninstaller.app.	macOS may prompt for admin rights.
Windows	Use Settings → Apps → Installed apps (or Control Panel → Programs and Features) and uninstall DeepPhe 7.1. You can also run uninstall.exe from the install directory, such as C:\DeepPhe\uninstall.exe.	Windows may request elevation.
Linux	Run the uninstall executable from the chosen install directory, for example cd <install dir> && ./uninstall.	If DeepPhe was installed in a system location such as /opt, run it with the privileges needed to remove that directory.

The uninstaller removes the program (.DeepPhe) and the launcher. It shows a checkbox to optionally also delete ~/DeepPheDocs:

Warning! Deleting DeepPheDocs will remove all input and output files in the directory. If you have patient reports or results in the DeepPheDocs directory, and you would like to keep the files on your machine, do not check the box.

Leave it unchecked to keep your data.