adding readme to index.md docs

docs/index.md

@@ -1,5 +1,80 @@
-# Calling Cards Tools
+# callingCardsTools
 
-This package is intended to provide both command line utilities as well as
-useful objects for the processing and analysis of Calling Cards sequencing
-data.
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10042067.svg)](https://doi.org/10.5281/zenodo.10042067)
+[![Test workflow](https://github.com/cmatKhan/callingCardsTools/actions/workflows/codecov.yml/badge.svg)](https://github.com/cmatKhan/callingCardsTools/actions/workflows/codecov.yml)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/callingcardstools/README.html)
+
+## 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](https://github.com/nf-core/callingcards) pipeline,
+which provides a workflow to process both yeast and mammals Calling Cards data.
+
+## Documentation
+
+[Served Documentation](https://cmatkhan.github.io/callingCardsTools/) provides
+information on filetypes and the API. For help with the cmd line tools,
+simply install callingcardstools (see below) and do:
+
+```bash
+callingcardstools --help
+```
+
+Each of the cmd line tools also provides a `--help` message.
+
+## Installation
+
+callingCardsTools is available through bioconda:
+
+```bash
+conda install -c bioconda callingcardstools
+```
+
+pypi:
+
+```bash
+pip install callingcardstools
+```
+
+or github (this will be the most current version):
+
+```bash
+pip install git+https://github.com/cmatkhan/callingCardsTools.git
+```
+
+After installing, you can get help with the cmd line tools by doing:
+
+```bash
+callingcardstools --help
+```
+
+## Callingcardstools is containerized:
+
+- A singularity container is hosted on
+  [Galaxyhub](https://depot.galaxyproject.org/singularity/). 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)](https://quay.io/repository/biocontainers/callingcardstools).
+  Again, make sure you get the correct version.
+
+## Development Installation
+
+1. install [poetry](https://python-poetry.org/)
+
+- 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.