                                                    Rheinfelden, Summer 2011

MIRA version 3.4.x


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


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
==========

If you downloaded a precompiled package, just put the binaries somewhere in
your path. Please read the documentation in the docs directory.

For source code packages, 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

additionally for user documentation as HTML and PDF: 

4) make docs


Directory structure of the source 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 sub-directories, 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.


Need help?
==========
Mail general questions to the MIRA talk mailing list:
        mira_talk@freelists.org

To report bugs or ask for new features, please use the new ticketing system at:
   http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests do not get lost.


Help wanted
===========
Do you want to help improving 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


