Installing MIRA

Bastien Chevreux

MIRA Version 3.4.1.1

Document revision $Id$

Table of Contents

1. Where to fetch MIRA
2. Installing from a precompiled binary package
3. Integration with third party programs (gap4, consed)
4. Compiling MIRA yourself
 

A problem can be found to almost every solution.

 
 --Solomon Short

1.  Where to fetch MIRA

SourceForge: http://sourceforge.net/projects/mira-assembler/

There you will normally find a couple of precompiled binaries -- usually for Linux, sometimes also for Mac OSX -- or the source package for compiling yourself.

Precompiled binary packages are named in the following way:

mira_miraversion_audience_OS-and-binarytype.tar.bz2

where

  • miraversion is usually a version number in three parts, like 3.0.5, sometimes also followed by some postfix like in 3.2.0rc1 to denote release candidate 1 of the 3.2.0 version of MIRA.

  • audience is either prod or dev; denoting either a production or a development version.

    The development version usually contains more checks and more debugging output to catch potential errors, hence it might run slower. Furthermore, development versions may contain some new code which did not get as extensive testing as usual.

  • OS-and-binarytype finally define for which operating system and which processor class the package is destined. E.g., linux-gnu_x86_64_static contains static binaries for Linux running a 64 bit processor.

Source packages are usually named

mira-miraversion.tar.bz2

Examples for packages at SourceForge:

  • mira_3.0.5_prod_linux-gnu_x86_64_static.tar.bz2
  • mira_3.0.5_prod_linux-gnu_i686_32_static.tar.bz2
  • mira_3.0.5_prod_OSX_snowleopard_x86_64_static.tar.bz2
  • mira-3.0.5.tar.bz2

2.  Installing from a precompiled binary package

Download the package, unpack it. Inside, there is -- beside other directories -- a bin. Copy or move the files and soft-links inside this directory to a directory in your $PATH variable.

Additional scripts for special purposes are in the scripts directory. You might or might not want to have them in your $PATH.

Scripts and programs for MIRA from other authors are in the 3rdparty directory. Here too, you may or may not want to have (some of them) in your $PATH.

3.  Integration with third party programs (gap4, consed)

MIRA sets tags in the assemblies that can be read and interpreted by the Staden gap4 package or consed. These tags are extremely useful to efficiently find places of interest in an assembly (be it de-novo or mapping), but both gap4 and consed need to be told about these tags.

Data files for a correct integration are delivered in the support directory of the distribution. Please consult the README in that directory for more information on how to integrate this information in either of these packages.

4.  Compiling MIRA yourself

Please follow the instructions in the INSTALL file on the top level of the source package.

Over time, things will be transferred to this help file.