Getting Started with pyaddons

version: 0.4.2b0

Misc additional utilities used on many of my scripts and repositories, individually not big enough to warrant a repository so all lumped together.

There is online documentation for pyaddons.

Installation instructions

pip install

At present, no packages exist yet on PyPy. Therefore, for pip install you should clone this repository and then cd to the root of the repository.

pip install cfin-pyaddons

Installation using conda

A conda build is also available for Python v3.8/v3.9/v3.10 on linux-64/osX-64. Although please note that all development and testing is performed in linux-64 (Python v3.9).

conda install -c conda-forge -c cfin -c bioconda cfin-pyaddons

Installing companion bash scripts

In addition to the Python command-line scripts that are available when the package is installed. There are also some bash scripts located in ./resources/bin. Please note these will not be installed when you install via clone & pip or a conda install. If using conda you will have to clone the repo. With either install method you will need to add the ./resources/bin directory to your PATH.

These scripts will require two bash libraries to be in your PATH.

1. shflags - This <https://github.com/kward/shflags>_ is to manage bash command line arguments.
2. bash-helpers - This <https://gitlab.com/cfinan/bash-helpers>_ wraps some handle bash functions.

For more information on what is available see the bash script documentation.