                                                    Rheinfelden, Winter 2014

README for the binary package of MIRA 4.0.x
===========================================

Table of contents
-----------------

1. What's new?
2. What's provided?
3. Installation
4. Documentation
5. Demos
6. License and Disclaimer
7. Contact


1. What's new?
==============

For a complete list of changes since a specific version, please consult
CHANGES.txt, or for older updates, src/mira/CHANGES_old.txt of the source
package distributions.

Current stable versions will have major.minor.sub-version of 4.0.x while
development version will have a branch identifier of 4.1.x.


2. What's provided?
===================

You have downloaded the binary package of MIRA. It consists of binaries,
documentation and support files.

Binaries provided:
 - mira: for assembly or mapping of sequences
 - miramem: estimating memory needed to assemble projects. Realised through
   link to the mira binary.
 - miraconvert: for converting sequencing related file types into other
   types. Includes various options for processing, filtering etc.pp. Realised
   through link to the mira binary.
 - mirabait: quickly bait sequences from a large set.Realised through link to
   the mira binary.
Note: the above is just only one binary ("mira"), the others are just soft
links pointing to mira.

Scripts provided:
 - fasta2frag.tcl: fragmenting sequences into smaller, overlapping
   subsequences. Useful for simulating shotgun sequences. Can create
   subsequences in both directions (/default) and also paired-end sequences.
 - fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
   consensus tags in ACE files written by the MIRA assembler (and possibly
   other programs). This script massages an ACE file so that consed can read
   the consensus tags.

Documentation provided:
See section 4 "Documentation"

Support files provided:
The support directory contains files for the Staden gap4/gap5 assembly viewer
and finishing tool which teaches the viewer about the tags MIRA uses. These
files are up-to-date and ready to use. The same files for "consed" should be
seen as "pointer to how things could be done" as I do not own consed to test
these files.


3. Installation
===============

The binaries (in directory "bin") are statically linked and self
contained, they should work with any Linux kernel >=2.6. On Mac OSX, they
may work on version 10.5 and should work on all versions >= 10.6.

Copy the binaries and the soft links (and scripts if you want) into a
directory in your path environment (or add the extraction directory to your
path variable) and you are ready to go.

Support files for the Staden GAP4 (GAP5) assembly finishing tool and consed
are in the "support" directory. Please refer to the documentation of the
respective package on how to integrate them into your environment.


4. Documentation
================

Documentation in HTML and PDF format can be found in the 'docs' directory.

Provided files:
 - DefinitiveGuideToMIRA.html
   Full documentation in HTML format
 - DefinitiveGuideToMIRA.pdf
   Full documentation in PDF format

If you are new to MIRA, I suggest you start reading the following chapters in
the full documentation:

 - Introduction (always)
 - Installation (eventually)
 - Preparing data
 - Then
    - De-novo assemblies
    - Mapping assemblies
    - EST / RNASeq assemblies
 - Working with the results of MIRA (always)
 - Utilities in the MIRA package (eventually)
 - Assembly of hard genome or EST projects (always)
 - Some advice when going into a sequencing project (eventually)

Vut it wouldn't hurt if you quickly looked at the tableof content of all the
other chapters to determine whether there might be something interesting for
you in it.


5. Demos
========

At the moment no demos are provided. However, the step by step documentation
and example configuration in the manual should get you going in no time.


6. Licenses and Disclaimer
==========================

The MIRA source code is under the GPL licence (currently v2). Permission to
use this software for any purpose is hereby granted without fee, but make sure
to stick to the GPL.

The documentation pertaining to MIRA is licensed under the Creative Commons
Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of
this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send
a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco,
California, 94105, USA.

Any version of this software and documentation is provided 'as-is', without
any express or implied warranty. In no event will the author be held liable
for any damages arising from the use of this software. Every kind of usage of
the software is only allowed with the acceptance of this license. 'Using'
certainly defines installing and running the software, it also includes
copying or providing the software or a service built upon its functionalities
for third-parties.

The author disclaims all warranties with regard to this software, in all
versions. Use it at your own risk.


7. Contact
==========

If you have any question regarding usage of MIRA, please subscribe to the MIRA
talk mailing list

  http://www.freelists.org/list/mira_talk

and then send your question to:

  mira_talk@freelists.org

To report bugs or ask for features, please use the ticketing system at:

  http://sourceforge.net/p/mira-assembler/tickets/

This ensures that requests don't get lost.

Home of MIRA: http://sourceforge.net/projects/mira-assembler/


Have a lot of fun with MIRA,
  Bastien
