Metadata-Version: 2.1
Name: scipion-em-gautomatch
Version: 3.2
Summary: Plugin to use Gautomatch program within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-gautomatch
Author: Grigory Sharov, J.M. De la Rosa Trevin
Author-email: sharov.grigory@gmail.com, delarosatrevin@scilifelab.se
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-gautomatch/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-gautomatch/
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: scipion-em

Gautomatch plugin
=================

This plugin provides a wrapper for Gautomatch picker developed by Kai Zhang at MRC LMB.

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

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

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

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

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

b) Developer's version

   * download repository 
   
   .. code-block::
   
      git clone -b devel https://github.com/scipion-em/scipion-em-gautomatch.git

   * install 

   .. code-block::
   
      scipion installp -p /path/to/scipion-em-gautomatch --devel

Gautomatch binaries will be installed automatically with the plugin, but you can also link an existing installation. 

Configuration variables
-----------------------

- CONDA_ACTIVATION_CMD: If undefined, it will rely on conda being in the PATH. An example of a conda activation cmd can be **eval "$(/extra/miniconda3/bin/conda shell.bash hook)"**.
- GAUTOMATCH_ENV_ACTIVATION: Command to activate the Gautomatch environment. This environment must have CUDA installed (cudatoolkit=10.1).
- GAUTOMATCH_HOME: Path to gautomatch binary containing folder (default = software/em/gautomatch-0.56)
- GAUTOMATCH_BIN: Specific binary to use (default = Gautomatch_v0.56_sm30-75_cu10.1)

Verifying
---------

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

``scipion test gautomatch.tests.test_protocols_gautomatch.TestGautomatchAutomaticPicking``

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

0.56

Protocols
---------

* `auto-picking <https://github.com/scipion-em/scipion-em-gautomatch/wiki/ProtGautomatch>`_

References
----------

1. Kai Zhang. Unpublished. 
