The easiest way to install atropos is to use pip on the command line:

pip install --user --upgrade atropos

This will download the software from PyPI (the Python packaging index), and install the atropos binary into $HOME/.local/bin. If an old version of atropos exists on your system, the --upgrade parameter is required in order to install a newer version. You can then run the program like this:

~/.local/bin/atropos --help

If you want to avoid typing the full path, add the directory $HOME/.local/bin to your $PATH environment variable.


Atropos can also be installed using conda:

conda install atropos


We provide a Docker container that can be executed using a Docker or Singularity engine:

docker run jdidion/atropos <args>


singularity run docker://jdidion/atropos

Manual installation


Atropos requires this software to be installed:

  • One of Python 3.3+.
  • A C compiler.
  • Cython 0.25.2+

Under Ubuntu, you may need to install the packages build-essential and python-dev.


If you have already downloaded and unpacked the .tar.gz file, then installation is done like this:

python3 install --user

If you get an error message:

error: command 'gcc' failed with exit status 1

Then check the entire error message. If it says something about a missing Python.h file, then you need to install the Python development packages. The appropriate package is called python3-dev in Ubuntu.sour

We also provide a Makefile that can optionally run unit tests for you. For this you will need to have make installed and also the Python pytest library (if you want to run the tests). To both test and install, run:

make installargs='--user'

To only install, run:

make install installargs='--user'

System-wide installation

If you have root access, then you can install atropos system-wide by running:

sudo pip install atropos

This installs atropos into /usr/local/bin.

If you want to upgrade from an older version, use this command instead:

sudo pip install --upgrade atropos

To use the Makefile, simply run:


or (to skip running tests)

make install

Use without installation

Build the C extension module (you can try to skip this step – a compiled version of the module for Linux x86_64 is already included):

python build_ext -i

Then simply run the script from where it is, similar to this:

bin/atropos --help

If you get any errors, first try to explicitly request a specific Python version by running atropos like this:

python3 bin/atropos --help