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Adding docker docs
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tjakobi committed Mar 6, 2023
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Expand Up @@ -12,7 +12,7 @@ Supported operating systems

``circtools`` was developed and tested on Debian Buster (10) and Ubuntu Jammy Jellyfish (22.04). macOS is supported, but still in development. However, macOS functionality cannot be fully guaranteed yet.

Installation from PyPi (preferred)
Installation via PyPi
-----------------------------------

The default installation will install everything needed to run circtools *except R, STAR, or Stringtie* (see below). If you like you may install circtools locally (first call) or globally (second call, SU required).
Expand All @@ -26,7 +26,27 @@ Please note:
* The required R libraries will be installed in the default location in your home directory - unless you set enviromnet variable $R_LIBS_USER.
* In case want to install globally or into a dedicated 'venv' drop the --user option.

Installation from GitHub
Installation via docker
-----------------------------------

Docker can be used as a simple alternative to install **circtools**, taking care of all Python and R dependencies, thus making it well-suited for novice users. The only requirement is a working docker installation. The following command will install the latest stable version of **circtools**:

.. code-block:: bash
docker pull jakobilab/circtools
Subsequently, **circtools** can be run via

.. code-block:: bash
docker run circtools [insert command args here]
.. code-block:: bash
Other than the additional command `docker run circtools` vs. just `circtools` all commands remain unchanged.


Installation via GitHub
--------------------------

The GitHub installation will install the most recent version directly from the source repository. Use this method if you want the latest fixes and features.
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