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XMapTools Installation & Update Guide

This guide covers how to install and update XMapTools 4.5 and future releases on macOS and Windows using the official bootstrap scripts. These scripts automate downloading, extracting, and configuring XMapTools and the required MATLAB Runtime.

Table of Contents

Prerequisites

RequirementmacOSWindows
OSmacOS (Intel or Apple Silicon)Windows 10/11
Admin rightsYes (script prompts for sudo password)Yes (run PowerShell as Administrator)
Internet connectionRequiredRequired
ShellTerminal (zsh or bash)PowerShell

Note: The MATLAB Runtime is installed automatically during a full installation. You do not need a MATLAB licence.

Compatibility: XMapTools 4.5 for Apple Silicon Macs requires MATLAB Runtime 25.1. XMapTools 4.5 for Windows and Intel-based Macs requires MATLAB Runtime v99 (R2020b). The older Runtime v912 can be safely deleted after updating to XMapTools 4.5. On Apple Silicon Macs, v99 can also be deleted.

Security: The code executed by the install command is available at https://xmaptools.ch/install.sh (macOS) and https://xmaptools.ch/install.ps1 (Windows). Do not use any other domain name. The xmaptools.ch domain is official and the only domain used to distribute XMapTools. If you are behind a firewall that blocks access, ask your system administrator to allow HTTPS traffic to this domain.


macOS

All macOS commands are run in the Terminal app. The script is fetched directly from the XMapTools server and executed locally.

Full Installation (macOS)

A full installation downloads XMapTools and the MATLAB Runtime. Use this when installing XMapTools for the first time or when you need to reinstall the runtime.

Auto-detect architecture (recommended):

bash
curl -fsSL https://xmaptools.ch/install.sh | bash -s -- --install

The script automatically detects whether your Mac uses Apple Silicon or Intel and downloads the correct version.

What happens during installation:

  1. Any previous XMapTools installation in /Applications/XMapTools is removed (you may be prompted for your administrator password).
  2. The installer archive is downloaded and extracted to a temporary directory.
  3. macOS Gatekeeper quarantine flags are cleared so the app can launch.
  4. The graphical installer opens — follow the steps below to complete the setup.
  5. A terminal command xmaptools is created so you can launch the app from any terminal window.

Graphical installer steps (macOS):

  1. Enter your password to allow the MATLAB Runtime Installer to make changes.
  2. Press Next.
  3. Leave the default installation folder /Applications/XMapTools to allow automatic updates in the future and press Next.
  4. Leave the default installation folder for the Runtime /Applications/MATLAB/MATLAB_Runtime and press Next.
  5. Click Begin Install to install XMapTools and download the Runtime (~2 GB).
  6. Press Close when the installation is complete.
  7. You can now start XMapTools using XMapTools.app.

Update Only (macOS)

An update replaces the XMapTools application bundle without reinstalling the MATLAB Runtime. This is faster than a full installation and preserves your runtime setup.

Prerequisite: XMapTools 4.5 or a more recent version running with Runtime 25.1 (Apple Silicon) or v99 (Intel) must already be installed in /Applications/XMapTools and must be closed.

Auto-detect architecture (recommended):

bash
curl -fsSL https://xmaptools.ch/install.sh | bash -s -- --update

What happens during an update:

  1. The script verifies that XMapTools is already installed.
  2. The latest application archive is downloaded and extracted.
  3. The previous app bundle (XMapTools.app) is replaced with the new version.
  4. Gatekeeper quarantine flags are cleared.
  5. Correct file permissions are set on user configuration files.
  6. Temporary files are cleaned up.

Show Information (macOS)

To display the available versions, remote file timestamps, detected MATLAB Runtime installations, and usage instructions:

bash
curl -fsSL https://xmaptools.ch/install.sh | bash -s -- --info

Architecture Selection (macOS)

OptionWhen to use
AppleSiliconMacs with M1, M2, M3, M4, or later Apple chips (native performance)
IntelMacs with Intel processors
(omitted)The script auto-detects the architecture — Apple Silicon is selected on arm64 hardware

Tip: If you are unsure which architecture your Mac uses, click > About This Mac. If the Chip field says "Apple M…", use AppleSilicon. If it says "Intel", use Intel.

Terminal Command (macOS)

After installation or update, the script creates a command-line launcher at /usr/local/bin/xmaptools. You can start XMapTools from any terminal by typing:

bash
xmaptools

The script also updates your shell configuration file (.zshrc, .bash_profile, or .profile) to ensure /usr/local/bin is on your PATH.


Windows

All Windows commands are run in PowerShell. You should run PowerShell as Administrator (right-click → Run as Administrator).

Full Installation (Windows)

A full installation downloads XMapTools and the MATLAB Runtime.

powershell
iex "& { $(irm https://xmaptools.ch/install.ps1) } --install"

What happens during installation:

  1. Any previous XMapTools installation in C:\Program Files\XMapTools is removed.
  2. The installer archive is downloaded and extracted to a temporary directory.
  3. The graphical installer (XMapToolsInstaller_Windows.exe) is launched — follow the on-screen instructions to complete the setup.

Graphical installer steps (Windows):

  1. Press Next.
  2. Leave the default installation folder Program Files/XMapTools to allow automatic updates in the future and press Next.
  3. Leave the default installation folder for the Runtime Program Files/MATLAB/MATLAB_Runtime and press Next.
  4. Click Begin Install to install XMapTools and download the Runtime (~3 GB).
  5. Press Close when the installation is complete.
  6. You can now start XMapTools using XMapTools.exe.

Update Only (Windows)

An update replaces the XMapTools executable and splash screen without reinstalling the MATLAB Runtime.

Prerequisite: XMapTools must already be installed in C:\Program Files\XMapTools.

powershell
iex "& { $(irm https://xmaptools.ch/install.ps1) } --update"

What happens during an update:

  1. The script verifies that XMapTools is already installed.
  2. The latest application archive is downloaded and extracted.
  3. XMapTools.exe (and splash.png if present) are copied into the existing installation directory.
  4. Temporary files are cleaned up.

Show Information (Windows)

To display the available version, remote file timestamps, detected MATLAB Runtime installations, and usage instructions:

powershell
iex "& { $(irm https://xmaptools.ch/install.ps1) } --info"

Troubleshooting

"XMapTools does not appear to be installed"

This error occurs when running --update without a prior installation. Run a full installation first:

  • macOS: curl -fsSL https://xmaptools.ch/install.sh | bash -s -- --install
  • Windows: iex "& { $(irm https://xmaptools.ch/install.ps1) } --install"

"Invalid MCR version" after updating

If XMapTools reports an invalid MATLAB Runtime version after an update, the runtime may have changed between versions. Perform a full reinstallation using --install to get the matching runtime.

MATLAB Runtime not found

The scripts check for the MATLAB Runtime in:

  • macOS: /Applications/MATLAB/MATLAB_Runtime
  • Windows: C:\Program Files\MATLAB\MATLAB Runtime

If the runtime is missing, a full installation (--install) is required.

Supported MATLAB Runtime versions

Runtime versionPlatform
v99 (R2020b)macOS Intel, Windows
R2025amacOS Apple Silicon (native)

macOS: "app is damaged" or Gatekeeper warning

The installation script automatically clears Gatekeeper quarantine flags. If you still see a warning, run manually:

bash
sudo xattr -cr /Applications/XMapTools/application/XMapTools.app

Windows: script execution policy

If PowerShell refuses to run the script, you may need to adjust the execution policy for the current session:

powershell
Set-ExecutionPolicy -Scope Process -ExecutionPolicy Bypass

Then re-run the installation or update command.

Windows: MATLAB Runtime 2025a conflict

If you already have MATLAB Runtime 2025a (R2025a) installed on your computer, you may receive an error message stating that the installer cannot connect to the MATLAB server. If this happens, open a Command Prompt window (cmd) as an administrator (right-click and select Run as administrator), then run:

cmd
cd C:\Program Files\MATLAB\MATLAB_Runtime
rmdir /s R2025a

Then re-run the XMapTools installation.

Windows: permission denied

Make sure you are running PowerShell as Administrator. Right-click the PowerShell icon and select Run as Administrator.

XMapTools suddenly not opening (Windows)

If XMapTools was working previously and suddenly stops opening, this can be caused by a corrupted MATLAB Runtime installation or a Windows update that modified system paths. Try the following:

  1. Perform a full reinstallation using the --install flag
  2. If the issue persists, uninstall the MATLAB Runtime (see Delete Old Runtime Libraries) and reinstall

Unfreeze XMapTools in case of error

If XMapTools becomes unresponsive during an operation, a dialog box may appear with OK and Cancel buttons. Click Cancel to cancel the current operation and unfreeze XMapTools. Clicking OK may restart the operation and keep XMapTools frozen.

Uninstalling XMapTools (Windows)

To fully uninstall XMapTools on Windows:

  1. Open Settings → Apps & Features (or Control Panel → Programs and Features)
  2. Find XMapTools in the list and click Uninstall
  3. Optionally, uninstall the MATLAB Runtime from the same list if no other MATLAB-based applications require it

Quick Reference

ActionmacOSWindows
Installcurl -fsSL https://xmaptools.ch/install.sh | bash -s -- --installiex "& { $(irm https://xmaptools.ch/install.ps1) } --install"
Updatecurl -fsSL https://xmaptools.ch/install.sh | bash -s -- --updateiex "& { $(irm https://xmaptools.ch/install.ps1) } --update"
Infocurl -fsSL https://xmaptools.ch/install.sh | bash -s -- --infoiex "& { $(irm https://xmaptools.ch/install.ps1) } --info"
Install dir/Applications/XMapToolsC:\Program Files\XMapTools
Runtime dir/Applications/MATLAB/MATLAB_RuntimeC:\Program Files\MATLAB\MATLAB Runtime

Delete Old Runtime Libraries

After upgrading to XMapTools 4.5 on an Apple Silicon Mac, the older MATLAB Runtime versions (v99, v912) are no longer needed and can be safely removed to free disk space.

Note: On Windows and Intel Macs, MATLAB Runtime v99 is still required. Do not delete it on these platforms.

macOS (Apple Silicon only):

bash
sudo rm -rf /Applications/MATLAB/MATLAB_Runtime/v99
sudo rm -rf /Applications/MATLAB/MATLAB_Runtime/v912

Windows:

Use Settings → Apps & Features (or Add or Remove Programs) to uninstall the older MATLAB Runtime versions (R2020b / v912).

XMapTools - Quantitative compositional mapping