README for the binary package of MIRA V2.8.x


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

1. What's new?
2. What's provided? 
3. Installation
4. Documentation
5. Demos
6. About 454 data
7. EMBOSS/EMBASSY integration
8. Contact



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

The 2.8.x series of MIRA is an intermediate step towards MIRA 3.0. However,
two major highlights (beside the usual stream of small improvements and
bugfixes) justify a new production release:

1) Important speedups in a few central places (Reads, Contigs). Additionally,
   the all-against-all read comparison algorithm (SKIM) has been speeded-up by
   a factor of >60 (for large number of reads).
2) MIRA is going Open Source! More specifically, MIRA is being put under the
   GPL (version 2) as I kindly received the authorisation from both the DKFZ
   Heidelberg (Deutsches Krebsforschungszentrum, German Cancer Research
   Center) and from Thomas Pfisterer (the author of the EdIt part in MIRA) to
   release the code.

Important notice: in preparation for the next version of MIRA, a few parameter
switches were had to be changed since the 2.6.x releases. Existing parameter
files may have to be adapted. Please consult the documentation for the new
parameters.

For a complete list of changes since a specific version, please consult
CHANGES.txt (included in this binary package) or CHANGES_old.txt (only
available in the source package).


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

The binary package consists of binaries, documentation, a directory with small
demos and a directory with some support files.

Binaries provided: 
 - mira: for assembly of genome sequences
 - miraEST: for assembly of EST sequences in different strains (link
   to mira executable)
 - uncover_at: for a preprocessing EST sequences (if wanted)
 - convert_project: for converting project file types into other types
 - caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
   file converters (realised through links to convert_project)
 - scftool: set of tools useful when working with SCF trace files
 - fastatool: set of tools useful when working with FASTA trace files

A template parameter file (paramtemplate.par) for MIRA is in the main
directory. It has all parameters in short form, but does NOT form a valid
parameter file in itself. It is meant as reference for if one wants to write
own parameter files.


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

The binaries (in directory "bin") are statically linked and self
contained, they should work with any Linux kernel >=2.6.

Copy the binaries 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 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.

You can install the ".1" manual files by copying them into a "man" directory of
your system.


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

Documentation in man, html and texinfo format can be found in the
'docs' directory. 

Provided files:
 - mira(.html|.1|.info)
 - mira_usage(.html|.1|.info)

The main documentation resides in the first file (mira...). If you are new to
MIRA, I suggest you read at least the short introduction in the
"mira_usage..." file. This will provide you a basic toolset for getting
started with MIRA.


5. Demos
========

A few small usage examples for genomic and EST assembly are in the
'minidemo' directory. As the demos rely on file links, this directory
will have to be unpacked under a Unix operating system. Unpacking it
with WinZip/WinRAR/other Windows applications and then transferring
the directory to Linux will NOT work.

Simply go into the directory and execute the runme.sh scripts (and have a look
at them if you wish).


6. About 454 data
=================

Please note that the 2.8 line does not officially support assembly of 454
data. These routines are (still) under development, parts of it are already in
included but not compiled in. This is scheduled for the 2.9 development line.


7. EMBOSS/EMBASSY integration
=============================

Integration of MIRA into the EMBOSS package as an EMBASSY application is work
in progress.


8. Contact
===========

If you have questions on how to use MIRA (or whether it can be used for a
specific task), comments, suggestions or if you find bugs, feel free to
contact me at

    bach@chevreux.org

Home of MIRA: http://www.chevreux.org/projects_mira.html


Bastien
