Table of Contents
“A problem can be found to almost every solution. ” | ||
--Solomon Short |
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
is usually
a version number in three parts, like miraversion
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.
is either
audience
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.
finally define for which operating system and which processor class
the package is destined. E.g.,
OS-and-binarytype
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
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.
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.