In principle, installing SIRIUS just means extracting the archive you have downloaded to an arbitrary directory where you have write permissions. 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 might require admin permissions. Since we do not pay Microsoft/Apple for certification you might have to confirm that you want to trust software from an unknown source on Windows/MacOS.

Further, Bright Giant is offering signed installers free of charge. These installers ease installation process a lot by triggering no (or less) security issues of the respective OS.

Completing the installation should take you not more than 10 minutes.

If you have trouble installing SIRIUS, please let us know and we will see if we can help. If you find that our installation guide is incomplete, or if you have some tricks that you want to share with your fellow scientists, please let us know, so we can include them in this manual, or even better, contribute them yourself.

Warning All advice given here on how to get SIRIUS running on your system, is given without any warranty! If you are not sure what you are doing, you might want to contact someone who does. (Remember, 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 have the option to choose an installation location and need to accept the SIRIUS license agreement. The installer should also create a start menu entry for SIRIUS.

##### Zip package

Extract the archive to an arbitrary directory where you have write permissions, such as C:\SIRIUS.

##### Execution

Go to the SIRIUS directory. Run sirius-gui.exe to start the graphical user interface. You might want to create a link on your desktop: Click and drag the file to the desktop, keeping the ALT key pressed. You can rename the link on your desktop as you like. You start SIRIUS by double-clicking this link.

Run sirius.exe for the SIRIUS command line tool. To execute the SIRIUS command line tool from every location on your system, you have to add the location of the sirius.exe to your PATH environment variable: Open the Windows Setting, 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 might be “hidden” under "System Settings" -> "Security & Privacy". This should not occur with the signed installer

Follow the instructions of the installer. You will have the option to choose an installation disk and need to accept the SIRIUS license agreement.

##### Zip package

Extract the archive to an arbitrary directory where you have write permissions, e.g. Download folder. You can then move/copy the extracted .app folder to your application directory. You might have to define gate keeper 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 just go to you app directory an double click the sirius-gui app. You can also add SIRIUS to your dock if you like.

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

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

/Applications/sirius.app/Contents/MacOS/


In case you have changed it, replace the line with the appropriate sirius installation dir. Note that the SIRIUS GUI versio also contains the command line runner, but uses a slieghly different location er default:

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


## Linux

Built and tested on Ubuntu 18.04+ x64

##### Zip version

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

To start the commandline 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 every location you have to add the <SIRIUS_DIR>/bin to your PATH variable. To do so, open in an editor and add the following line (replacing the placeholder path) to your ~/.bashrc:

export PATH=PATH:<SIRIUS_DIR>/bin/


Note that you have to reopen your “bash” shell to make the changes effective.

## User account and License (since v5.0.0)

Certain features of SIRIUS require access to the SIRIUS web services; this includes structure elucidation with CSI:FingerID and CANOPUS. From version 5 on, using these features requires a license and a user account. The SIRIUS web services are free for academic/non-commercial use. Usually academic institutions are identified by their email domain and access will be granted automatically. In some cases, further validation might be required.

See Account and License for further information about licensing and account creation.

## Installing Gurobi and/or CPLEX

SIRIUS ships with the COIN-OR Integer Linear Program solver which allows us to swiftly compute fragmentation trees in most cases. However, if you want to analyze large molecules and/or spectra with many peaks and/or many spectra, you can improve running time by using a faster solver. SIRIUS also supports Integer Linear Program solvers Gurobi and CPLEX. These are commercial solvers which offer a free academic license for university members. You can find installation instruction on their websites. Using Gurobi or CPLEX will improve the speed of fragmentation tree computations, which is the most time-intense step of the computational analysis. Besides, there will be no differences in using Gurobi, 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 solver if corresponding environment variables are specified. You can specify the preferred solvers in the settings dialog (GUI) or when running 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 modify the following line to your needs:

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


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

## Proxy servers

To use web service functionality of SIRIUS, it needs an internet connection. You have to ensure that SIRIUS is not blocked by any security software on your computer.

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

If SIRIUS cannot connect to the Internet, it will report on which stage the error occurred.

## System Requirements

• OS: Windows 10+, MacOS, Linux
• CPU: Dual Core x86-64 (Quad Core x86-64 is recommended)
• RAM: 4GB (2GB per CPU core is recommended)
• Internet: 1Mbit/s is recommended