zongzhiwu / glimps

A User-Friendly Pipeline for the production of Core Genome and Concatenated Protein based Phylogenetic Trees and Protein based Comparative Genomic Analyses

The Gupta Lab Integrated Microbial Phylogeny and Supermatrix (GLIMPS) Pipeline

A User-Friendly Pipeline for the production of Core Genome and Concatenated Protein based Phylogenetic Trees and Protein based Comparative Genomic Analyses.

Installation

1. Download the latest release and extract to a local directory.
2. Use chmod +x to make dependencies executable in Linux and OSX (dependencies should be executable by default in Windows).
3. Use python GLIMPS_Pipeline.py to run the pipeline without the GUI from the Terminal or Command Line (requires Python 2.7 or newer).
4. Use sudo apt-get install python-tk to install the Tkinter module required for the GLIMPS GUI in Linux (Tkinter should be included in the default installation of Python 2.7 in OSX and Windows).
5. If Python is set as your default program for .py files, double click GLIMPS_UI.py to start the GLIMPS GUI. If not, run python GLIMPS_UI.py from the Terminal or Command Line to start the GLIMPS GUI.

Command Line Usage

python GLIMPS_Pipeline.py [options] or python GLIMPS_UI.py

Use command line argument -h to obtain a detailed list of arguments.

Usage Guide

Coming Soon...

History

Version 0.8:

• Parallelized AAI calculation
• Numerous Bugfixes

Version 0.5:

• Initial Public Test Release

Credits

Mobolaji Adeolu (Department of Biochemistry and Biomedical Sciences, McMaster University)

License

GNU GENERAL PUBLIC LICENSE v3 Copyright (c) 2016 Mobolaji Adeolu