Copyright (C) 2018 Arthur Zwaenepoel

VIB/UGent center for plant systems biology - Bioinformatics & evolutionary genomics group http://bioinformatics.psb.ugent.be/beg/

wgd - simple command line tools for the analysis of ancient whole genome duplications

Installation

Python package and command line interface (CLI) for the analysis of whole genome duplications (WGDs). Tested with Python3.5 & Python3.6 on Linux Ubuntu. If you don't have python or pip installed a simple sudo apt-get install python3-pip should do.

To install: clone the repo, navigate to it and install it with pip

$ git clone https://github.com/arzwa/wgd.git
$ cd wgd
$ pip install .

Note that depending on your python installation and whether you're in a virtualenv, pip may default either to pip2 or pip3. If the above installation step fails, please try to use pip3 instead of pip.

For the command line interface, upon installation run

$ wgd

to get a list of the available commands. To get usage instructions for a command (e.g. ksd) run

$ wgd ksd --help

For external software requirements: please consult the relevant section in the docs: https://wgd.readthedocs.io/en/latest/index.html#external-software

To use as a Python package as well as to find additional documentation and examples for the CLI, please consult the docs at http://wgd.readthedocs.io/en/latest/

Singularity container

A singularity container is available for wgd, allowing all to use all tools in wgd except wgd syn, without having to install all required software on your system. To install Singularity follow the instructions here

If you have singulaity installed (and you're in the virtual machine when running on Windows or Mac), you can run (from within the cloned repository)

sudo singularity build wgd.simg wgd.shub

to build the container. Then you can use wgd as follows

singularity exec wgd.simg wgd <command>

Notes

Bug tracking: If the program crashes, exits unexpectedly or some unexpected results are obtained, please run it again with the --verbosity debug flag before the subcommand of interest (e.g. wgd --verbosity debug ksd gf.mcl cds.fasta). If the anomaly persists, please open an issue on this GitHub site.

Note on input data: while the input data is rather straightforward (a CDS fasta file will do for most analyses) it may be of interest that the wgd suite was extensively tested with data from the PLAZA platform, so for examples of the right input data formats (in particular CDS fasta files for sequence data and GFF files for structural annotation), please have a look there.

Note on virtualenv: you can install wgd in a virtual environment (using virtualenv). If you would however encounter problems with running the executable directly (e.g. wgd --help doesn't work) you can circumvent this by directly calling the CLI, using python3 ./wgd_cli.py --help (assuming you are currently in the directory where you cloned wgd).

Citation

Please cite us at https://doi.org/10.1093/bioinformatics/bty915

Arthur Zwaenepoel, Yves Van de Peer; wgd - simple command line tools for the analysis of ancient whole genome duplications, 
Bioinformatics, , bty915, https://doi.org/10.1093/bioinformatics/bty915

For citation of the tools used in wgd, please consult the documentation at https://wgd.readthedocs.io/en/latest/index.html#citation.