callingCardsTools 1.1.0

A collection of objects and functions to work with calling cards sequencing tools

Introduction

CallingCardsTools Provides both an API and a number of cmd line tools for processing raw Calling Cards data. This is used in the nf-core/callingcards pipeline, which provides a workflow to process both yeast and mammals Calling Cards data.

Documentation

Served Documentation provides information on filetypes and the API. For help with the cmd line tools, simply install callingcardstools (see below) and do:

callingcardstools --help

Each of the cmd line tools also provides a --help message.

Installation

pip install callingcardstools

To start using the command line tools, see the help message with:

callingcardstools --help

Callingcardstools is containerized:

docker pull cmatkhan/callingcardstools

singularity pull cmatkhan/callingcardstools

Development Installation

1. install poetry

• I prefer to set the default location of the virtual environment to the project directory. You can set that as a global configuration for your poetry installation like so: poetry config virtualenvs.in-project true

2. git clone the repo

3. cd into the repo and issue the command poetry install

4. shell into the virtual environment with poetry shell

5. build the package with poetry build

6. install the callingcardstools package into your virtual environment pip install dist/callingcardstools-...

• Note: you could figure out how to use the pip install -e flag to have an interactive development environment. I don't think that is compatible with only the pyproject.toml file, but if you look it up, you'll find good stackoverflow instructions on how to put a dummy setup.py file in to make this possible