1. Installation¶

1.1. Requirements¶

NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/docs/v1/quickstarts/command-line-tools/)

1.2. GTAX with Python virtual environment¶

1.2.1. GTAX python installation¶

Python 3.7 or above should be installed.

localhost:~> python3 -m venv gtax_venv
localhost:~> source gtax_venv/bin/activate
(pm4ngs_venv) localhost:~> pip install wheel
(pm4ngs_venv) localhost:~> pip install gtax

1.2.2. GTAX python env activation¶

For activating the virtual env:

localhost:~> source gtax_venv/bin/activate
(pm4ngs_venv) localhost:~> gtax -v
GTAX version: 0.0.1

1.3. GTAX with Conda/BioConda¶

1.3.1. Conda installation¶

Conda should be already installed and configured using these commands:

localhost:~> wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
localhost:~> sh Miniconda3-latest-Linux-x86_64.sh
localhost:~> conda config --add channels defaults
localhost:~> conda config --add channels bioconda
localhost:~> conda config --add channels conda-forge

1.3.2. GTAX conda installation¶

GTAX should be installed in a Conda virtual environment named gtax:

localhost:~> conda create -n gtax gtax

1.3.3. GTAX conda env activation¶

For activating the conda env:

localhost:~> conda activate gtax
localhost:~> gtax -v
GTAX version: 0.0.1