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: 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