installation-on-macos.md

macOS

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Install via macOS installer

To install OpenMS on macOS, run the following steps:

1. Download and install the macOS drag-and-drop installer from the archive. 2.Double click on the downloaded file. It will start to open the OpenMS-<version>-macOS.pkg installer file.

:alt: macOS warning message when opening OpenMS-<version>-macOS.pkg
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Why This Warning Appears:

The warning indicates that the OpenMS installer hasn't been notarized or recognized by Apple as being from an identified developer. This doesn't necessarily mean the software is unsafe; it simply means that macOS cannot verify its source. support.apple.com

How to Proceed:

Bypassing Gatekeeper to Install OpenMS on macOS

A. Bypassing Gatekeeper Using System Settings

1. Open System Settings.
2. Navigate to Privacy & Security.
3. Under the Security section, locate the message about the blocked application.
4. Click the Open Anyway button .

:alt: Bypassing Gatekeeper on macOS
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B. Bypassing Gatekeeper Using Command-Line

For users comfortable with the command line, you can bypass the security warning using Terminal:

1. Open Terminal.

2. Navigate to the directory containing the installer using the cd command:

   cd /path/to/installer

3. Run the following command to remove the quarantine attribute:

   xattr -d com.apple.quarantine OpenMS-<version>-macOS.pkg

By following these steps, you’re instructing macOS to trust the OpenMS installer and allow its execution. Ensure that you’ve downloaded the installer from a trusted source (i.e., build archive of the Unversity of Tübingen or OpenMS' GitHub artifacts) before proceeding.

4. Install OpenMS

:alt: OpenMS installation started on macOS
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5. Agree to the license agreements.

:alt: License agreement
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6. Installation Confirmation

:alt: OpenMS installation successful
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To use {term}TOPP as regular app in the shell, add the following lines to the ~/.profile file.

:::{warning} Known Installer Issues

1. Nothing happens when you click OpenMS apps or the validity of the developer could not be confirmed.

   This usually means the OpenMS software lands in quarantine even after installation of the .pkg. This was more common with our older .dmg image but may still happen. Since macOS Catalina (maybe also Mojave) all apps and executables have to be officially notarized by Apple but we currently do not have the resources for a streamlined notarization workflow.

   To have a streamlined experience without blocking popups, it is recommended to remove the quarantine flag manually, using the following steps:

   Open the Terminal.app and type the following (replace the first line with the actual installation directory):

   cd /Applications/OpenMS-<version>
   sudo xattr -r -d com.apple.quarantine *

2. Bug with running Java based thirdparty tools like {term}MSGFPlusAdapter and {term}LuciphorAdapter from within TOPPAS.app

   If you face issues while running Java based thirdparty tools from within {term}TOPPAS.app <TOPPAS>, run the {term}TOPPAS.app <TOPPAS> from within the Terminal.app (e.g. with the open command) to get access to the path where Java is located. Java is usually present in the PATH of the terminal. Advanced users can set this path in the Info.plist of/inside the TOPPAS.app.

   export OPENMS_TOPP_PATH=<OpenMS-PATH>
   source ${OPENMS_TOPP_PATH}/.TOPP_bash_profile

   Make sure <OpenMS-PATH> points to the folder where OpenMS is installed locally (e.g., /Applications/OpenMS-<version>)

:::

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Build OpenMS from source

To build OpenMS from source, follow the build instructions for macOS.