                                                    Rheinfelden, July 28th 2007

Provisional README

MIRA - The Genome and EST Sequence Assembly System
EdIt - An Automatic Assembly Editing Tool


Important
=========
The 2.8.x series of MIRA is NOT able to work with 454 data. Please use the
current development version (2.9.x) for testing 454 assembly with MIRA.


License
=======

Since version 2.8.0, MIRA (and the therein contained version of EdIt) is
licensed under the open source GPL v2 license. please consult the "COPYING"
file for more information on the GPL.


Installing
==========

Please consult the file INSTALL for more information on pre-requisites and
available options. There's also a section on building documentation in the
same file.

Here's a short summary:

Note: if you are working on a CVS checkout, you need to have GNU
autoconf/automake tools and run "sh runme.first" from the top-level directory
first.

Then, in the best case, building MIRA binaries is done in three steps (but
please consult the INSTALL file before doing so):

1) ./configure
2) make
3) make install

(User documentation is not built through this!)


Directory structure of the package
==================================

Top level (this level): 
- standard files from GNU autoconf and automake as well as README; INSTALL,
  etc.
- directory "src": the MIRA sources. Type "make" to make the binaries.
- directory "doc": the MIRA documentation in LaTeXMAN format. Use "make docs"
  to build the documentation in HTML, man and texinfo format.
- directory "distribution": type "make distrib" and a package is made that
  contains binaries, documentation and some demos
- directory "minidemo": a few demos for mira and miraEST. PLease note that the
  demos are not directly usable in this directory and that one should never
  try to run mira or miraEST in that directory. The reason is that "make
  distrib" will make a complete copy of this directory
- directories "miratest" and "test": please disregard these directories, they
  just contain a few toy test cases used in development of MIRA.

For more information on the subdirectories, please consult the README files
there (if present).


Programming with MIRA
=====================

The overall code documentation is not good. While it is slowly brought up to
speed, please have a look at the files in ./src/examples_programming. And then
look at the public functions of the classes in the .src/mira directory.


Help wanted
===========
Do you want to improve MIRA? Please consult the HELP_WANTED file.


Author:
=======
MIRA - Bastien Chevreux: bach@chevreux.org

EdIt - mira can use automatic editing routines which were written by Thomas
       Pfisterer: t.pfisterer@dkfz-heidelberg.de

