deviaTE is a python tool for the analysis and visualization of mobile genetic element sequences. It is available for Unix and Linux systems.
The recommended way of using deviaTE is in a conda virtual environment. This way, all dependencies should be resolved.
Create a new conda virtual environment, and install deviaTE:
conda create deviaTE -c r -c defaults -c conda-forge -c bioconda -c w-l -n deviaTE_env
this command loads all required anaconda channels (r, defaults, conda-forge, bioconda, w-l) and names the environment deviaTE_env
The environment can then be activated, and deviaTE with all necessary dependencies can be used inside the environment:
source activate deviaTE_env
After using deviaTE, the environment can be exited using:
source deactivate
DeviaTE can also be installed with the pip python package manager. However, this does not take care of all dependencies. The following tools need to be set up manually beforehand:
- python 3.6+
- pip for python3 (https://pip.pypa.io/en/stable/installing/)
- samtools (tested with version 1.6 and 1.9)
- bwa (tested with version 0.7.17)
- R (tested with version 3.4.3)
- required R packages are installed automatically upon first usage
samtools and bwa need to be in your $PATH
DeviaTE can then be installed with
pip3 install deviaTE
conda environment:
conda env remove -n deviaTE_env
pip package:
pip3 uninstall deviaTE
A manual and a walkthrough with examples using publicly available data can be found here:
A paper describing deviaTE is available here:
@article{weilguny2019,
author = {Weilguny, Lukas and Kofler, Robert},
title = {{DeviaTE}: {Assembly-free} analysis and visualization of mobile genetic element composition},
journal = {Molecular Ecology Resources},
volume = {Accepted Author Manuscript},
year= {2019},
doi = {10.1111/1755-0998.13030}
}
If you find any problems, have questions or ideas for further improvement please use the issue tracker on this repository, thanks!
deviaTE is licensed under the GPLv3 License