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__ __ _ _
| \/ |_ _ _ __ __ _ ___ __ _| | _(_)
| |\/| | | | | '__/ _` / __|/ _` | |/ / |
| | | | |_| | | | (_| \__ \ (_| | <| |
|_| |_|\__,_|_| \__,_|___/\__,_|_|\_\_|
* Requirements
Boost (http://www.boost.org/) to build/run the core Murasaki algorithm
** Optional requirements
Perl (http://www.perl.org/) to assist in the build process and to
interface with some of the optional packages described below.
CryptoPP (http://www.cryptopp.com/) (optional, but enabled by default)
provides CPU specific enhancements. If you don't want to use CryptoPP
you can disable it any of the following ways: compiling via a command
like "make WITH_LIBCRYPTOPP=NO"
* setting WITH_LIBCRYPTOPP=NO as an environment variable before running make
* setting WITH_LIBCRYPTOPP=NO somewhere in the Makefile
MPI. To use Murasaki in a cluster, you'll need some implementation of
MPI. While Murasaki should be implementation agnostic, we've done
most of our testing and tuning on OpenMPI (http://www.openmpi.org/)
MPICH (http://www.mcs.anl.gov/mpi/mpich/) and MPICH-MX
(http://www.myri.com/scs/download-mpichmx.html) are also tested and
known to work.
Murasaki interfaces with a lot of other free software to generate
graphs and statistical information. To use all the features of
Murasaki, you should also have:
- BioPerl (http://www.bioperl.org/) is required by the annotation
reading parts of the perl scripts.
- R (http://www.r-project.org/)
-- ROCR (http://rocr.bioinf.mpi-sb.mpg.de/)
- gnuplot (http://www.gnuplot.info/)
- ImageMagick (http://www.imagemagick.org/)
* Build instructions
Building under a debian based system (the intended audience) is very
easy. Make sure you have the appropriate packages installed:
-On Debian lenny: aptitude install libboost-dev libcrypto++-dev g++ make perl
-On Debian squeeze: aptitude install libboost-all-dev libcrypto++-dev g++ make perl
-On Mac OS X: port install gcc42 boost libcryptopp
-- We recommend using Mac Ports (http://www.macports.org/) to get/build these libraries/packages
If your system is already set up, once you've download one of the
above packages, the following should work:
cd murasaki
make
In general, the included Makefile should find everything it needs
automatically (including detecting whether or not you have Crypto++
and an MPI compiler available), but if something fails, or something
isn't detected automatically, feel free to edit the Makefile
accordingly. If all else fails, email us
(murasaki-users@lists.sourceforge.net) and we'll see what we can do to
help.
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