Start:
* What's Murasaki? [#b825e248]
Murasaki is an anchor alignment program that is
- exteremely fast (17 CPU hours for whole Human x Mouse g...
- scalable (Arbitrarily parallelizable across multiple no...
- memory efficient. (Even a single node with 16GB of ram ...
- unlimited by pattern length or selection
- repeat tolerant
* Compatability [#p624f2ab]
Targeted for runs on 32/64bit Linux and other POSIX compa...
Tested on:
- Debian (lenny, squeeze)
- FreeBSD 6, 7
- MacOS X 10.4, 10.5, 10.6
- Ubuntu 9.10
- Fedora 12
With some luck, sometimes working in win32 with mingw, bu...
*License [#f2a78a64]
Murasaki is distributed under the [[GNU General Public Li...
**Download [#a4261a72]
Murasaki download packages are available in [[Murasaki do...
Or, keep up with the latest release using
[[Mercurial>http://mercurial.selenic.com/]]:
hg clone http://murasaki.hg.sourceforge.net:8000/hgroot/...
Subversion support is deprecated, but technically still e...
** Requirements [#wbb904d1]
- [[Boost>http://www.boost.org/]] to build/run the core M...
** Optional requirements [#d50b1479]
- [[Perl>http://www.perl.org/]] to assist in the build pr...
- [[CryptoPP>http://www.cryptopp.com/]] (optional, but en...
-- If you don't want to use CryptoPP you can disable it a...
--- compiling via a command like "make WITH_LIBCRYPTOPP=NO"
--- setting WITH_LIBCRYPTOPP=NO as an environment variabl...
--- setting WITH_LIBCRYPTOPP=NO somewhere in the Makefile
- MPI. To use Murasaki in a cluster, you'll need some imp...
-- While Murasaki should be implementation agnostic, we'v...
-- [[MPICH>http://www.mcs.anl.gov/mpi/mpich/]] and [[MPIC...
Murasaki interfaces with a lot of other free software to ...
- [[BioPerl>http://www.bioperl.org/]] is required by the ...
- [[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 [#k4306574]
Building under a debian based system (the intended audien...
-On Debian lenny: aptitude install libboost-dev libcrypto...
-On Debian squeeze: aptitude install libboost-all-dev lib...
-On Ubuntu [karmic,lucid]: aptitude install libboost-dev ...
-On Mac OS X: port install gcc42 boost libcryptopp
-- We recommend using [[Mac Ports>http://www.macports.org...
If your system is already set up perfectly, once you've d...
+'''cd murasaki'''
+'''make'''
In general, the included Makefile should find everything ...
** Getting started [#s8febe0f]
Most of the documentation for Murasaki currently exists i...
There's also a manpage in doc/murasaki.1 (or the .html or...
An example Murasaki run might go like this:
|'''./murasaki seq/MtC.gbk seq/Mle.gbk -p[28:36] -b24 --n...
|'''./simplegraph.pl output/myalignment.anchors'''|This g...
Obviously this is just a sample run. You're strongly enco...
** Sample alignments [#v752c56d]
As an example of some of the huge alignments Murasaki is ...
Be aware, however, that these alignments can be huge (for...
** Documentation [#h73944ea]
Documentation is still a work in progress. For now please...
** Citation [#u21c93cc]
If you use Murasaki in your work, please cite our [[PLoS ...
- Popendorf K, Tsuyoshi H, Osana Y, Sakakibara Y (2010) M...
End:
* What's Murasaki? [#b825e248]
Murasaki is an anchor alignment program that is
- exteremely fast (17 CPU hours for whole Human x Mouse g...
- scalable (Arbitrarily parallelizable across multiple no...
- memory efficient. (Even a single node with 16GB of ram ...
- unlimited by pattern length or selection
- repeat tolerant
* Compatability [#p624f2ab]
Targeted for runs on 32/64bit Linux and other POSIX compa...
Tested on:
- Debian (lenny, squeeze)
- FreeBSD 6, 7
- MacOS X 10.4, 10.5, 10.6
- Ubuntu 9.10
- Fedora 12
With some luck, sometimes working in win32 with mingw, bu...
*License [#f2a78a64]
Murasaki is distributed under the [[GNU General Public Li...
**Download [#a4261a72]
Murasaki download packages are available in [[Murasaki do...
Or, keep up with the latest release using
[[Mercurial>http://mercurial.selenic.com/]]:
hg clone http://murasaki.hg.sourceforge.net:8000/hgroot/...
Subversion support is deprecated, but technically still e...
** Requirements [#wbb904d1]
- [[Boost>http://www.boost.org/]] to build/run the core M...
** Optional requirements [#d50b1479]
- [[Perl>http://www.perl.org/]] to assist in the build pr...
- [[CryptoPP>http://www.cryptopp.com/]] (optional, but en...
-- If you don't want to use CryptoPP you can disable it a...
--- compiling via a command like "make WITH_LIBCRYPTOPP=NO"
--- setting WITH_LIBCRYPTOPP=NO as an environment variabl...
--- setting WITH_LIBCRYPTOPP=NO somewhere in the Makefile
- MPI. To use Murasaki in a cluster, you'll need some imp...
-- While Murasaki should be implementation agnostic, we'v...
-- [[MPICH>http://www.mcs.anl.gov/mpi/mpich/]] and [[MPIC...
Murasaki interfaces with a lot of other free software to ...
- [[BioPerl>http://www.bioperl.org/]] is required by the ...
- [[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 [#k4306574]
Building under a debian based system (the intended audien...
-On Debian lenny: aptitude install libboost-dev libcrypto...
-On Debian squeeze: aptitude install libboost-all-dev lib...
-On Ubuntu [karmic,lucid]: aptitude install libboost-dev ...
-On Mac OS X: port install gcc42 boost libcryptopp
-- We recommend using [[Mac Ports>http://www.macports.org...
If your system is already set up perfectly, once you've d...
+'''cd murasaki'''
+'''make'''
In general, the included Makefile should find everything ...
** Getting started [#s8febe0f]
Most of the documentation for Murasaki currently exists i...
There's also a manpage in doc/murasaki.1 (or the .html or...
An example Murasaki run might go like this:
|'''./murasaki seq/MtC.gbk seq/Mle.gbk -p[28:36] -b24 --n...
|'''./simplegraph.pl output/myalignment.anchors'''|This g...
Obviously this is just a sample run. You're strongly enco...
** Sample alignments [#v752c56d]
As an example of some of the huge alignments Murasaki is ...
Be aware, however, that these alignments can be huge (for...
** Documentation [#h73944ea]
Documentation is still a work in progress. For now please...
** Citation [#u21c93cc]
If you use Murasaki in your work, please cite our [[PLoS ...
- Popendorf K, Tsuyoshi H, Osana Y, Sakakibara Y (2010) M...
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