Metadata-Version: 2.1
Name: scipion-em-aretomo
Version: 3.0.10
Summary: Plugin to use AreTomo program within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-aretomo
Author: Grigory Sharov
Author-email: sharov.grigory@gmail.com
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-aretomo/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-aretomo/
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Requires-Dist: scipion-em

==============
AreTomo plugin
==============

This plugin provides a wrapper for `AreTomo <https://msg.ucsf.edu/software>`_ program.

.. image:: https://img.shields.io/pypi/v/scipion-em-aretomo.svg
        :target: https://pypi.python.org/pypi/scipion-em-aretomo
        :alt: PyPI release

.. image:: https://img.shields.io/pypi/l/scipion-em-aretomo.svg
        :target: https://pypi.python.org/pypi/scipion-em-aretomo
        :alt: License

.. image:: https://img.shields.io/pypi/pyversions/scipion-em-aretomo.svg
        :target: https://pypi.python.org/pypi/scipion-em-aretomo
        :alt: Supported Python versions

.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-aretomo?server=https%3A%2F%2Fsonarcloud.io
        :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-aretomo
        :alt: SonarCloud quality gate

.. image:: https://img.shields.io/pypi/dm/scipion-em-aretomo
        :target: https://pypi.python.org/pypi/scipion-em-aretomo
        :alt: Downloads

Installation
------------

You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:

a) Stable version

.. code-block::

    scipion installp -p scipion-em-aretomo

b) Developer's version

    * download repository

    .. code-block::

        git clone https://github.com/scipion-em/scipion-em-aretomo.git

    * install

    .. code-block::

        scipion installp -p /path/to/scipion-em-aretomo --devel

AreTomo binaries will be installed automatically with the plugin, but you can also link an existing installation. 
Default installation path assumed is ``software/em/aretomo-1.0.12``, if you want to change it, set *ARETOMO_HOME* in ``scipion.conf`` file to
the folder where the AreTomo is installed. Depending on your CUDA version you might want to change the default binary from ``AreTomo_1.0.12_Cuda101``
to a different one by explicitly setting *ARETOMO_BIN* variable. If you need to use CUDA different from the one used during Scipion installation
(defined by CUDA_LIB), you can add *ARETOMO_CUDA_LIB* variable to the config file. Various binaries can be downloaded from the official UCSF website.

To check the installation, simply run the following Scipion test:

``scipion test aretomo.tests.test_protocols_aretomo.TestAreTomo``

Licensing
---------

AreTomo is free for academic use only. For commercial use, please contact David Agard or Yifan Cheng for licensing:

    * agard@msg.ucsf.edu
    * Yifan.Cheng@ucsf.edu

Supported versions
------------------

1.0.6, 1.0.8, 1.0.10, 1.0.12

Protocols
---------

    * tilt-series align and reconstruct

Detailed manual can be found in ``software/em/aretomo-1.0.12/bin/AreTomoManual-01-27-2022.pdf``

References
----------

    * AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction. Shawn Zheng, Georg Wolff, Garrett Greenan, Zhen Chen, Frank G. A. Faas, Montserrat Bárcena, Abraham J. Koster, Yifan Cheng, David Agard. bioRxiv 2022.02.15.480593; doi: https://doi.org/10.1101/2022.02.15.480593


