Metadata-Version: 1.1
Name: transphire
Version: 1.4.18
Summary: Automated post data aquisition processing tool
Home-page: https://github.com/mstabrin/transphire
Author: Markus Stabrin
Author-email: markus.stabrin@tu-dortmund.de
License: GPLv3
Description: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1419991.svg)](https://doi.org/10.5281/zenodo.1419991)
        
        
        
        
        # Transphire
        
        Cryo-EM on the fly processing pipeline.
        
        If you have any questions contact:  
        markus.stabrin@mpi-dortmund.mpg.de
        
        ## External programs
        
        To enjoy the full functionaly of TranSPHIRE, install the following programs:
        
        IMOD 4.9: http://bio3d.colorado.edu/imod  
        MotionCor2 1.0.0/1.0.5/1.1.0: http://msg.ucsf.edu/em/software/motioncor2.html  
        SumMovie 1.0.2: http://grigoriefflab.janelia.org/unblur  
        CTER 1.0: http://sphire.mpg.de  
        CTFFIND 4.1.8/4.1.10: http://grigoriefflab.janelia.org/ctf  
        Gctf 1.06,1.18: https://www.mrc-lmb.cam.ac.uk/kzhang  
        crYOLO 1.0.4/1.0.5/1.1.0: http://sphire.mpg.de  
        
        ## Installation
        
        TranSPHIRE needs an environment that includes Python version 3.6, QT version 5 and PyQt version 5.
        
        ### Installation using Anaconda
        
        https://www.anaconda.com/download/#linux
        
        Create a new virtual environment
        
        > conda create -n transphire python=3.6 pyqt=5
        
        Activate the environment
        
        > source activate transphire
        
        or
        
        > conda activate transphire
        
        Depending on your installation of anaconda.
        
        Install transphire
        
        > pip install transphire
        
        
        ### Installation inside your own environment that matches the requirements
        
        Install transphire
        
        > pip install transphire
        
        
        ## Run TranSPHIRE
        
        Make sure, that you have your transphire environment active.
        If you start TranSPHIRE for the first time:
        
        > transphire --edit\_settings
        
        In case the appearing window is too large for your screen, adjust the font size (default 20).  
        For example:
        
        > transphire --edit\_settings --font 8
        
        First got to the **TranSPHIRE settings** tab and after that the **Font** tab.
        Adjust the *Font* value.
        If necessary, the other options can be adjusted at a later point, after the GUI is opened.
        
        Open the other tabs and adjust the settings according to your system.
        
        Close the dialog and the GUI will open.
        
        In the future, you only need to run:
        
        > transphire
        
        If you want to run TranSPHIRE, fill in the tabs from left to right (General to CTF) and press the Start button.
        
        A more detailed tutorial will be available soon.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.6
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: POSIX :: Linux
Classifier: Environment :: X11 Applications :: Qt
Classifier: Development Status :: 4 - Beta
