add README

README

+=======================================================================
+Release notes for Meteor Version 3.2
+=======================================================================
+
+Files and directories
+=====================
+In the package, files are organized as follows:
+
+  -+- README:    This file
+   |
+   +- COPYING:   License
+   |
+   +- AUTHORS:   List of authors
+   |
+   +- data_preparation_tools/ --> programs dedicated to data preparation  
+   |
+   +- meteor-pipeline/ --> sources and other files to build the Meteor pipeline.
+      |
+      +- src/ --> c++ sources and makefile.
+      |
+      +- meteor.rb:   ruby source file.
+
+
+======================================================================
+Installation notes for Meteor Version 3.2
+======================================================================
+
+	This file describes the building and installation instructions from the SOURCES for UNIX like systems.
+	NB: Building and running Meteor on MS Windows system has not been tested,
+	    but should easily be achieved as Meteor uses standard C++ code without any exotic dependencies.
+
+Supported Systems
+=================
+
+	Will work in most modern GNU/Linux, and macOS (10.5 or later with Intel processor) systems.
+
+Building and running pre-requisite
+==================================
+
+	1. Compiler collections with c++98 support (e.g. g++ or clang++)
+
+	2. Ruby interpreter version 1.9 or later, with "inifile" rubygem module version 3.0.0 or later
+
+	3. bowtie2 version 2.3.5.1 or later, and bowtie 1.2.3 or later if you plan to use color space SOLiD data.
+
+Installation
+============
+
+	On a GNU/Linux system, we recommand to have g++, make and ruby installed via the package manager of your distribution.
+	e.g.:
+	
+	on Debian/Ubuntu plateforms (as root or sudoer):
+	apt-get install make g++ ruby
+	
+	on Redhat/Fedora/CentOS plateforms (as root or sudoer):
+	yum install make gcc-c++ ruby
+
+	- To build Meteor, open a terminal and execute the following commands:
+	
+	cd meteor-pipeline/src/
+	make
+	
+	This will create two binaries (meteor-counter and meteor-profiler) in the folder meteor-pipeline/src/build/
+	
+	- Now copy the meteor pipeline executables in a folder present in the PATH environment variable.
+
+	e.g. as root or sudoer (this will install meteor for all user):
+	cp build/meteor-counter build/meteor-profiler ../meteor.rb /usr/local/bin
+
+	Or as common user (every user of meteor will have to do this):
+	[ ! -d ~/bin ] && mkdir ~/bin
+	cp build/meteor-counter build/meteor-profiler ../meteor.rb ~/bin
+
+	- Then install the ruby module inifile (>= 3.0.0).
+	
+	As root or sudoer:
+	gem install inifile
+
+	As common user (every user of meteor will have to do this):
+	gem install inifile --user-install
+
+
+======================================================================
+Usage of Meteor Version 3.2
+======================================================================
+
+Data preparation
+================
+
+Use the program MeteorReferenceBuilder.rb to create the bowtie index of the reference gene catalog(s)
+Then organize the sample data with MeteorImportFastq.rb or MeteorImportCSFastaQual.rb
+
+These programs are located in the folder data_preparation_tools/
+
+Using Meteor 
+============
+
+   meteor.rb [list_of_arguments]
+   meteor-profiler [list_of_arguments]
+
+meteor.rb drives the mapping and counting processes for one sample.
+So launch as many instance of meteor.rb as the number of samples in your project.
+Then use meteor-profiler to gather the counting results of all samples in a unique matrix.
+
+NOTE: It is necessary to include the executable directory in the PATH environment variable.
+
+See Meteor quick start documentation for more details.
+