macOS

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.dmg disk image file.

3. Verify the download.

4. Agree to the license agreements.

5. Drag OpenMS to the Applications folder.

6. It will start copying to applications.

To use TOPP as regular app in the shell, add the following lines to the ~/.profile file.

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>)

Install via Conda or Bioconda

Follow the instructions .

Known 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 after installation of the .dmg. 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 MSGFPlusAdapter and LuciphorAdapter from within TOPPAS.app

   If you face issues while running Java based thirdparty tools from within TOPPAS.app, run the TOPPAS.app 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.