Ac update readme (#367)

* Have updated README

* Removed Andreas copyright

* formatting errors

* small changes to README

* Update README.rst

Updated links as per sebastians conversation

*  SLV comments

* link to conda

*  add latest contributors

README.rst

@@ -5,52 +5,77 @@
     :target: http://bioconda.github.io/recipes/cgat-scripts/README.html
 
 ===========================
-The CGAT code collection
+The CGAT Code Collection
 ===========================
 
-The CGAT code collection has grown out of the work in comparative
-genomics by the Ponting group in the last decade. Now, CGAT_ has added
-functionality to do next-generation sequencing analysis.
+The CGAT_ Code Collection has two components. The first component
+is a collection of scripts in this repository, which are located
+`here <https://github.com/CGATOxford/cgat/tree/master/CGAT/scripts>`_
+and can be run using the ``cgat`` command. Within this repository we also have a
+number of utility modules that help working with various file formats
+in Python. These are located `here <https://github.com/CGATOxford/cgat/tree/master/CGAT>`_.
 
-The CGAT Code collection has two components. The first component
-is a collection of scripts, the CGAT tools. The second component
-is a collection of pipelines. While both components are part of this
-collection, we are currently concentrating on publishing the CGAT
-tools.
+The second component is a collection of pipelines that utilise the
+functionality of the scripts and can be accessed
+`here <https://github.com/CGATOxford/CGATPipelines>`_.
 
-For questions, please subscribe and contact us at the 
-`CGAT user group
-<https://groups.google.com/forum/?fromgroups#!forum/cgat-user-group>`_.
+For questions, please open a discussion on the GitHub 
+`issue page <https://github.com/CGATOxford/cgat/issues>`_.
 
 Documentation of CGAT tools is available 
-`here <http://www.cgat.org/downloads/public/cgat/documentation/cgat.html#cgat>`_.
+`here <https://www.cgat.org/downloads/public/cgat/documentation/>`_.
 
-CGAT Tools
-==========
+Installation
+============
 
-The CGAT tools can be installed from pypi::
+Install using Conda
+-------------------
+
+The preferred method to install the CGAT code collection is using the installation script, which uses
+`Conda <https://conda.io>`_.
+
+Here are the steps::
+
+        # download installation script:
+        curl -O https://raw.githubusercontent.com/CGATOxford/cgat/master/install-CGAT-tools.sh
+
+        # see help:
+        bash install-CGAT-tools.sh
+
+        # install set of production scripts (well tested):
+        bash install-CGAT-tools.sh --production [--location </full/path/to/folder/without/trailing/slash>]
+
+        # or go for the latest development version:
+        bash install-CGAT-tools.sh --devel [--location </full/path/to/folder/without/trailing/slash>]
+
+The installation script will put everything under the specified location. The aim of the script is to
+provide a portable installation that does not interfere with the existing software. As a result, you
+will have a conda environment working with the CGAT scripts which can be enabled on demand according 
+to your needs.
+
+
+Install using pip
+-----------------
+
+You can also use pip to install the CGAT scripts. To go down this route, please type::
 
    pip install cgat
 
-To use CGAT Tools, use the ``cgat`` front-end. For example, to
-strip sequence and quality information from a bam_ file, type:
+However, CGAT depends on numerous other python packages which themselves might require
+manual intervention. Therefore, our preferred method of installation is through conda. 
 
-   cgat bam2bam --strip=sequence < in.bam > out.bam
 
-CGAT Pipelines
-==============
+Usage
+=====
 
-We have developed numerous pipelines in comparative genomics
-and NGS analysis. The pipelines are generally available and should
-be fairly portable. Some documentation of the pipelines is 
-`here <http://www.cgat.org/downloads/public/cgat/documentation/Pipelines.html#pipelines>`_.
+Run the ``cgat --help`` command to see what scripts are available and how to use them.
+For example, to strip sequence and quality information from a bam_ file, type::
 
-Note that we currently are not able to fully support and document the 
-pipelines. They are under continuous development and changing rapidly.
-However, they might give some ideas or building blocks when developing
-your own pipelines.
+   cgat bam2bam --strip=sequence < in.bam > out.bam
+
+For more extensive examples please refer to the documentation 
+`here <https://www.cgat.org/downloads/public/cgat/documentation/CGATReference.html>`_
 
 .. _bam: http://en.wikipedia.org/wiki/SAMtools
 .. _CGAT: http://www.cgat.org
 
-

THANKS.txt

@@ -9,6 +9,13 @@ Jethro Johnson
 Antonio Berlanga-Taylor
 Katherine Fawcett
 Xiaoming Hu
+Thomas Smith
+Michael Morgan
+Katherine Brown
+Charlotte George
+Adam Cribbs
+Hania Pavlou
+Sebastian Luna-Valero
 
 The CGAT code collection has been made possible by the many developers
 in the bioinformatics and python community that have made their code

doc/conf.py

@@ -66,7 +66,7 @@
 
 # General information about the project.
 project = u'CGAT'
-copyright = u'2011, 2012, 2013, 2014, 2015 Andreas Heger'
+copyright = u'2011, 2012, 2013, 2014, 2015, 2016, 2017 CGAT'
 
 
 # Included at the end of each rst file