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Installation

Welcome to the installation page of TranSPHIRE. The installation can be divided into three parts.

  1. Installation of TranSPHIRE
  2. Installation of the dependencies
  3. Basic TranSPHIRE setup

The TranSPHIRE version changelog can be found here:

  1. changelog-page

Installation of TranSPHIRE

In order to install TranSPHIRE it is highly recommended to setup an / environment. The same installation can be used to install crYOLO and other dependencies later. In case you want to learn more about environments: Manage environments.

After successful installation, the command should be available. To make things easier for copy and pasting, the proposed commands utilize bash variables. The installation does usually not take longer than a few minutes.

  1. Specify Necessary variables

>>> TRANSPHIRE_ENV_NAME=transphire

  1. Create a environment

>>> conda create -n ${TRANSPHIRE_ENV_NAME} python=3.6 pyqt=5

  1. Activate the environment

>>> conda activate ${TRANSPHIRE_ENV_NAME}

Note

For older versions of conda it might be:

>>> source activate ${TRANSPHIRE_ENV_NAME}

  1. Install TranSPHIRE

>>> pip install transphire

  1. Test the installation

>>> transphire --version

Installation of the dependencies

TranSPHIRE is a wrapper for already existing software packages available. Therefore, it is necessary to install the dependencies separately. In the future, we will work on a dependency installer tool.

Utilities and packages

  • version >= 1.4 / version >= 2.31
  • version >= 4.9
  • version >= 1.0 -

Note

The installation automatically installs all necessary tools for

  • Particle extraction
  • 3D initial model estimation
  • 3D refinement

and installs utility programs from the EMAN2 package.

Note

The installation needs one additional command to function properly:

>>> bash ${SPHIRE_INSTALL_DIR}/utils/replace_shebang.sh

This script will replace the shebang line of the executables to avoid collision with other python interpreters in your PATH.

Note

for the installation, you need to make sure that the IMOD source file is sourced in order to run properly.

Motion correction

  • version >= 1.0.0 -
  • cisTEM version >= 1.0.0-beta

CTF estimation

  • version >= 4.1.8
  • version >= 1.06

Note

GCtf version 1.18 is sometimes behaving different than expected. Use with caution.

Particle picking

  • version >= 1.0.4 -

Note

cannot be installed within the TranSPHIRE anaconda environment. Fortunately, this is not a problem, due to the total independence of anaconda environments. After following the installation instructions of and installed it in a seperate environment just deactivate the environment and activate the TranSPHIRE environment again. Just provide the link to the executable file in the TranSPHIRE GUI. Those are usually located in ${_CONDA_ROOT}/envs/CRYOLO_ENV_NAME/bin. The information how and in which environment to execute the respective executables is provided in the header. Alternatively, the directory path ${_CONDA_ROOT}/envs/CRYOLO_ENV_NAME/bin can be added to the PATH variable.

2D classification

  • version >= 2.3.1

2D class selection

  • version >= 0.3.1

Note

cannot be installed within the TranSPHIRE anaconda environment. Fortunately, this is not a problem, due to the total independence of anaconda environments. After following the installation instructions of and installed it in a seperate environment just deactivate the environment and activate the TranSPHIRE environment again. Just provide the link to the executable file in the TranSPHIRE GUI. Those are usually located in ${_CONDA_ROOT}/envs/CINDERELLA_ENV_NAME/bin. The information how and in which environment to execute the respective executables is provided in the header. Alternatively, the directory path ${_CONDA_ROOT}/envs/CINDERELLA_ENV_NAME/bin can be added to the PATH variable.