Installation
============

SDePER currently supports only Linux operating systems such as Ubuntu, and is compatible with Python versions 3.9.12 up to but not including 3.11.

SDePER can be installed using conda, pip or Docker/Singularity.


.. attention::

   It is recommended to **install SDePER using conda or pip** because of the observed incompatibility between `Numba <https://numba.pydata.org/>`_ and Docker/Singularity. When running SDePER in a Docker or Singularity container, a significant increase in running time was noticed, as Numba cannot fully utilize the CPU resources for parallel computing.


Install SDePER
--------------

.. tabs::

   .. tab:: conda

      .. code-block:: bash

         conda create -n sdeper-env -c bioconda -c conda-forge python=3.9.12 sdeper

   .. tab:: pip

      .. code-block:: bash

         conda create -n sdeper-env python=3.9.12
         conda activate sdeper-env
         pip install sdeper

   .. tab:: Docker

      .. code-block:: bash
         :substitutions:

         docker pull az7jh2/sdeper:|cur_version|

   .. tab:: Singularity

      .. code-block:: bash
         :substitutions:

         singularity build sdeper-|cur_version|.sif docker://az7jh2/sdeper:|cur_version|


Test installation
-----------------

It should print the version.

.. tabs::

   .. tab:: conda

      .. code-block:: bash

         runDeconvolution -v

   .. tab:: pip

      .. code-block:: bash

         runDeconvolution -v

   .. tab:: Docker

      .. code-block:: bash
         :substitutions:

         docker run -it --rm az7jh2/sdeper:|cur_version| runDeconvolution -v

   .. tab:: Singularity

      .. code-block:: bash
         :substitutions:

         singularity exec sdeper-|cur_version|.sif runDeconvolution -v


After installing SDePER using any one of these methods, you can start using the package. Please check out :doc:`usage` page for commands for cell type deconvolution and imputation. The detailed descriptions of all options in commands are in :doc:`cli_options` page, and a guidance on setting the options is in :doc:`best_practice` page.