In principle, installing SIRIUS is as simple as extracting the downloaded archive to a directory where you have write permission. The Java Runtime Environment (JRE) needed to run SIRIUS is already included.

For Windows/MacOS we also provide installer packages (msi/pkg), which should be preferred but may require admin permissions. As we do not pay Microsoft/Apple for certification, you may need to confirm that you want to trust software from an unknown source on Windows/MacOS.

The installation should take no more than 10 minutes.

If you have any problems installing SIRIUS, please contact support or ask for help in the community. You can also use the forum to let us know if you find that our installation guide is incomplete, or if you have tricks that you would like to share with other SIRIUS users. Feel also free to contribute to this documentation yourself.

WARNING: Any advice given here on how to get SIRIUS to work on your system is given without warranty! If you are not sure what you are doing, please contact someone who is. (Remember, the last Friday in July is System Administrator Appreciation Day!)

Windows

Built and tested on Windows 10 x64

MSI installer (preferred)

Execute the installer, trust the unknown source (if asked) and follow the instructions. You will be asked to choose an installation location and to accept the SIRIUS license agreement. The installer should also create a start menu entry for SIRIUS.

Zip package

Extract the archive to any directory where you have write permissions, e.g. C:\SIRIUS.

Execution

Go to the SIRIUS directory. Run sirius-gui.exe to start the graphical user interface. You may want to create a shortcut on your desktop: Click and drag the file to the desktop while holding down the ALT key. You can rename the desktop shortcut. Double-click it to start SIRIUS.

Run sirius.exe for the SIRIUS command line tool. To execute the SIRIUS command line tool from anywhere on your system, you must add the location of the sirius.exe to your PATH environment variable: Open the Windows Settings, type “advanced” in the search window, say “yes” if Windows asks you. Press the “Environment Variables” button, select the “Path” variable in the lower panel, press “Edit”, press “New”, enter the full directory path of SIRIUS, press RETURN. Close the Command Prompt, open a new one, type sirius.

Mac OSX

Built and tested on macOS Catalina 10.15 x64

pkg installer (preferred)

Execute the installer, trust the unknown source (if blocked by Gatekeeper). The option to confirm the execution of an installer from an unknown source may be “hidden” in "System Settings" -> "Security & Privacy". This should not happen with the signed installer

Follow the installer’s instructions. You will be asked to select an installation disk and to accept the SIRIUS licence agreement.

Zip package

Extract the archive to any directory where you have write permissions, e.g. the Download folder. You can then move/copy the extracted .app folder to your application directory. You may need to define gatekeeper exceptions for all libraries in the SIRIUS .app directory. If you are not sure how to do this we recommend using the installer version.

Execution

To run the SIRIUS GUI, simply go to your Applications directory and double-click the sirius-gui application. You can also add SIRIUS to your Dock if you prefer.

To run the SIRIUS command line tool, open a terminal and execute the sirius launcher in your Applications directory (usually /Applications/sirius.app/Contents/MacOS/sirius).

To execute SIRIUS from any location, you need to add the sirius binary directory <SIRIUS_DIR>/Contents/MacOS to your PATH variable. To do this, open /etc/paths in a text editor and add the following line:

/Applications/sirius.app/Contents/MacOS/

If you have changed the directory, replace the line with the respective sirius installation directory. Note that the SIRIUS GUI version also contains the command line runner, but uses a slightly different location per default:

/Applications/sirius-gui.app/Contents/MacOS/

Linux {linux}

Built and tested on Ubuntu 18.04+ x64

Zip version {zip-linux}

Extract the archive to any directory where you have write permissions, e.g. /home/opt/sirius.

To start the command line version of SIRIUS, execute the <SIRIUS_DIR>/bin/sirius starter in the terminal.

To start the graphical user interface of SIRIUS, execute the <SIRIUS_DIR>/bin/sirius-gui starter in the terminal.

To execute SIRIUS from any location, you must add the <SIRIUS_DIR>/bin to your PATH variable. To do this, open it in an editor and add the following line (replacing the placeholder path) to your ~/.bashrc:

export PATH=PATH:<SIRIUS_DIR>/bin/

Note that you will need to reopen your “bash” shell for the changes to take effect.

User account and License (since v5.0.0)

Certain features of SIRIUS require access to the SIRIUS web services:

  • structure elucidation with CSI:FingerID,
  • compound classification with CANOPUS,
  • de novo structure generation with MSNovelist.

From version 5 onwards, a licence and a user account are required to use these features. The SIRIUS web services are free for academic use. Academic institutions are identified by their email domain and access will be granted automatically. In case further validation is required, see Account and License.

Installing Gurobi and/or CPLEX

SIRIUS comes with the COIN-OR integer linear program solver which allows us to swiftly compute fragmentation trees in most cases. However, if you are analysing large molecules and/or spectra with many peaks and/or many spectra, you can improve running time by using a faster solver. SIRIUS supports the Gurobi and CPLEX integer linear program solvers. These are commercial solvers that offer a free academic licence for university members. Installation instructions can be found on their websites. Using Gurobi or CPLEX will improve the speed of the fragmentation tree computation, which is the most time-consuming step of the computational analysis. Other than that, there is no differences when using Gurobi or CPLEX. To use Gurobi, set the environment variable GUROBI_HOME to a valid Gurobi installation location. Similarly, to use CPLEX, set CPLEX_HOME to a valid Gurobi installation location.

CPLEX: On Windows, the CPLEX installer usually sets the system variable automatically, and you should be good to go.

  • Windows: set CPLEX_HOME to e.g. C:\Program Files\IBM\ILOG\CPLEX_Studio1271\cplex.
  • Linux: Set CPLEX_HOME to the CPLEX install directory e.g. /opt/ibm/ILOG/CPLEX_Studio1271/cplex.
  • MacOS: Set CPLEX_HOME to the CPLEX install directory e.g. /Library/ibm/ILOG/CPLEX_Studio1271/cplex.

Gurobi:

  • Windows: Set GUROBI_HOME to the Gurobi lib directory e.g. C:\gurobi702\win64.
  • Linux: Set GUROBI_HOME to the Gurobi lib directory e.g. /opt/gurobi702/linux64.
  • MacOS: Set GUROBI_HOME to the Gurobi lib directory e.g. /Library/gurobi702/mac64.

SIRIUS will automatically detect Gurobi or CPLEX as possible solvers if the respective environment variables are specified. You can specify the preferred solver in the settings dialogue (GUI) or in the command line with the --ilp-solver parameter. To permanently change the setting (e.g. for SIRIUS version 4.6.x) open: <USER_HOME>/.sirius-4.6/sirius.properties and edit the following line as required:

de.unijena.bioinf.sirius.treebuilder.solvers = cplex,gurobi,clp

The order of the solvers specifies the priority in which SIRIUS uses them.

Error message: “Could not load a valid TreeBuilder (ILP solvers), tried ‘[GUROBI, CPLEX, CLP, GLPK]’. Please read the installation instructions.” SIRIUS ships with the non-commercial CLP solver and should work out-of-the box. If you are nevertheless experiencing this issues, please contact us. It is almost impossible to reproduce and fix such issues without additional information from users. Thanks.

Proxy servers

To use the web service functionality of SIRIUS, an internet connection is required. You must ensure that SIRIUS is not blocked by any security software on your computer.

If you need to use a proxy server to connect to the Internet, you can specify the proxy configuration in the Sirius user interface settings (see Settings).

If SIRIUS cannot connect to the Internet, it will report at what stage the error occurred.

System Requirements

  • OS: Windows 10+, MacOS, Linux
  • CPU: Quad Core CPU (x86-64) is recommended (native Apple Silicon support only via conda package)
  • RAM: 8GB (2GB per CPU core is recommended)
  • Internet: 1Mbit/s is recommended