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Ticlla Ccenhua Monica Roxana authored
re-arrange TACOS as a package and add optimized functions for computation of Hamming-based pairwise genetic distances
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TACOS

TACOS is a diverse Set Of Commands And Tools (SOCAT, but TACOS sounds much better!) to handle genomic-derived data.

Basic setup

Create virtual environment

$ conda update conda
$ conda create --prefix=<path/tacos_env> -c intel intelpython3_core python=3.6.* icu=58 pandas scipy numpy joblib matplotlib
$ conda activate <path/tacos_env>
$ conda install -c conda-forge python-igraph tqdm pycairo
$ conda install -c bioconda gffutils

Install Tacos:

$ conda activate <path/tacos_env> # if not already activated
$ git clone https://git.scicore.unibas.ch/TBRU/tacos.git
$ cd tacos
$ pip install -e .

Run the application:

$ conda activate <path/tacos_env> # if not already activated
$ tacos --help

or

$ <path/tacos_env>/bin/python -m tacos --help # no need to activate the environment

To run the tests:

$ pytest tests