scipion-em-gautomatch 3.2.1

Plugin to use Gautomatch within the Scipion framework

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

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:

1. Stable version

   scipion installp -p scipion-em-gautomatch

2. Developer’s version

   • download repository

   git clone -b devel https://github.com/scipion-em/scipion-em-gautomatch.git

   • install

   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

References

1. Kai Zhang. Unpublished.