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Amirsadra Mohseni edited this page Jan 31, 2026 · 4 revisions

First Flight

SIRIUS was developed to work with Python 3.10.0+ and the following Linux distros: ALT Linux 10+, RHEL 9+, Debian 11+, Fedora 34+, Mageia 8+, Photon OS 3.0 with updates, and Ubuntu 21.04+ - SIRIUS is available on PyPI

Install SIRIUS with pip install sirius-bio and check everything works sirius --help

For a demo run, do sirius to run in interactive mode. Press Enter for all prompts to use defaults for all inputs, and check your results under sirius_output/.

Splashdown

Should you wish to uninstall SIRIUS, before uninstalling, run sirius --purge-cache (or after uninstall: rm -rf ~/.cache/sirius) to remove the cached Python 2.7 environment (which SIRIUS unpacks to use the dependency GeneDiversifier). Then, run pip uninstall sirius-bio -y

A Simple Constellation of Genes

There are two ways to run SIRIUS. The first and simplest is via the command line with flags. Pass your protein sequences as the first argument, then -n, and the desired number of gene sequences. For example:

sirius MALEEINENSTERN -n 6

When finished, a new folder will be created by the name "sirius_out" inside of which there will be three text files:

  • The sequences file contains your designed gene sequences
  • The length_counts file contains sorted fragment lengths and their number of occurrences within pairs of sequences
  • The summary file contains a brief summary of your run

The second way to run SIRIUS is by simply running the program interactively with sirius which will then prompt you to input your protein, number of desired sequences, and other parameters.

SIRIUS does not replace/overwrite your previous results. New outputs will have a counter added to the end of the folder name.

To programmatically download the protein sequences of the seven genes provided in the publication, see and run download_seq.ipynb

Note that by default, SIRIUS takes a minimum of 5 minutes to generate your results unless it finds an optimal solution. This time constraint may be increased or decreased with the -t parameter, as described in advanced settings.

Note that we recommend running SIRIUS on a high-memory HPC due to its computational requirements for longer sequences and higher copy numbers.

Proceed to basic settings to discover more.

Go to 1. Home, 2. Tutorial (Basic Settings), 3. Tutorial (Advanced Settings), or Code

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