callingCardsTools

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

callingCardsTools is available through bioconda:

conda install -c bioconda callingcardstools

pypi:

pip install callingcardstools

or github (this will be the most current version):

pip install git+https://github.com/cmatkhan/callingCardsTools.git

After installing, you can get help with the cmd line tools by doing:

callingcardstools --help

Callingcardstools is containerized:

• A singularity container is hosted on Galaxyhub. If you go to this site, make sure the ‘c’s have loaded and then search for ‘callingcardstools’. There is a container for each version which is on bioconda. Make sure you get the correct version.

• A docker container is hosted on quay (and biocontainers). Again, make sure you get the correct version.

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. you can pip install -e . to install the package in editable mode. This is useful if you want to test the cmd line interface as you make changes to the source code.