update docs

.readthedocs.yml

@@ -7,7 +7,7 @@ version: 2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
+  configuration: docs/source/conf.py
 
 # Build documentation with MkDocs
 #mkdocs:

docs/source/index.rst

@@ -15,6 +15,7 @@ __ homepage_
    :maxdepth: 2
    :caption: Contents:
 
+   introduction
    API
    CLI
 

docs/source/introduction.md

@@ -0,0 +1,34 @@
+# Introduction
+![pydamage logo](../img/logo.png)
+
+[![pydamage CI](https://github.com/maxibor/pydamage/workflows/pydamage_ci/badge.svg)](https://github.com/maxibor/pydamage/actions) [![Documentation Status](https://readthedocs.org/projects/pydamage/badge/?version=latest)](https://pydamage.readthedocs.io/en/latest/?badge=latest)
+
+Pydamage, is a Python software to automate the process of contig damage identification and estimation.
+It uses a process akin to a likelihood ratio test to attempt to discriminate between truly ancient, and modern contigs originating from sample contamination.
+
+## Install
+
+Pydamage is not yet on *pypi* nor *conda*, but you can already install it using pip, provided that you have access to this repository.
+
+### Install dependencies in conda environment
+
+```bash
+git clone git@github.com:maxibor/pydamage.git
+cd pydamage
+conda env create -f environment.yml
+conda activate pydamage
+```
+
+### Install pydamage
+
+- from source
+
+```bash
+python setup.py install
+```
+
+- from Github using pip
+
+```bash
+pip install git+ssh://git@github.com/maxibor/pydamage.git
+```