Develop -> Master repo README update

README.md

@@ -0,0 +1,69 @@
+[![Docs](https://readthedocs.org/projects/asap-modules/badge/)](https://readthedocs.org/projects/asap-modules)
+[![Code cov](https://codecov.io/gh/AllenInstitute/asap-modules/branch/master/graph/badge.svg?token=nCNsugRDky)](https://codecov.io/gh/AllenInstitute/asap-modules)
+
+# ASAP-modules
+
+ASAP is a set of modules to perform stitching and alignment of EM and Array tomography data.
+It is suitable for processing large-scale datasets and supports multiple computational environments.
+
+# Documentation
+
+The complete documentation is available [here](https://asap-modules.readthedocs.io)
+
+
+# Installation
+
+Please refer the documentation [Installation](docs/readme/installation.rst). on how to install and use ASAP modules
+
+# How to run
+
+The order of processing is as follows; 
+
+1. [Lens correction](docs/readme/lens_correction.rst)
+
+2. [Mipmap generation](docs/readme/mipmaps.rst)
+
+3. [Montaging](docs/readme/montaging.rst)
+
+4. [Global 3D alignment](docs/readme/rough_alignment.rst)
+
+# Other Modules
+
+A few other modules are included in ASAP to do the following.
+
+1. Materialization - render intermediate/final aligned volume to disk
+   for further processing
+2. Fusion - Fuse global 3D non-linear aligned chunks together to make a
+   complete volume
+3. Point match filter - A module that performs point match filtering of
+   an existing point match collection
+4. Point match optimization - Performs a parameter sweep from a given
+   set of ranges on a random sample of tilepairs to identify the optimal
+   set of parameters
+5. Registration - Register individual sections in an already aligned
+   volume (useful in cases of aligning missing/reimaged sections)
+
+.. _support:
+# Support
+
+
+We are planning on occasional updating this tool with no fixed schedule. 
+Community involvement is encouraged through both issues and pull requests. 
+Please make pull requests against the dev branch, as we will test changes 
+there before merging into master.
+
+.. _acknowledgements:
+# Acknowledgments
+
+This project is supported by the Intelligence Advanced Research Projects
+Activity (IARPA) via Department of Interior / Interior Business Center
+(DoI/IBC) contract number D16PC00004. The U.S. Government is authorized
+to reproduce and distribute reprints for Governmental purposes
+notwithstanding any copyright annotation theron.
+
+Disclaimer: The views and conclusions contained herein are those of the
+authors and should not be interpreted as necessarily representing the
+official policies or endorsements, either expressed or implied, of
+IARPA, DoI/IBC, or the U.S. Government.
+
+[![Docs](https://readthedocs.org/projects/asap-modules/badge/)](https://asap-modules.readthedocs.io)

docs/README.rst

@@ -10,7 +10,7 @@ It is suitable for processing large-scale datasets and supports multiple computa
 Installation
 ############
 
-Please refer the documentation :doc:`here </readme/installation>` on how to install and use ASAP modules 
+Please refer the documentation :ref:`Installation:Installation`. on how to install and use ASAP modules 
 
 How to run
 ##########