Installing SpikeOMatic on Linux
The R package
Good news it is straightforward
You might have to be logged on as root to do that, depending on the R
installation you want to work with (one in your home folder or one in
the /usr/local folder).
Once you have figured out if you need to be root or not, go to the
directory where you downloaded SpikeOMatic_0.5-1.tar.gz an
type the following shell command:
R CMD INSTALL SpikeOMatic_0.5-1.tar.gz
The C routines will be compiled and everything will get installed
where it should (e.g., on my machine in:
/usr/local/lib/R/library/SpikeOMatic/).
Other required packages
In order to make full use of the GUIs of SpikeOMatic you will need
some additional R packages from BioConductor.
These packages are:
- tkWidgets
- widgetTools
- DynDoc
You will find instructions on how to install them on the BioConductor
web site.
Some advices
Following an advice from Pascal Viot I got a very significant increase
in my codes speed (30 to 50% !) by using intel C compiler icc
rather than
GNU C compiler gcc. The intel compilers are
free for Linux so
you should think of using them. For instance the R version I'm running
on my machines is compiled from the source using icc and
ifc (the intel fortran compiler).
After compiling R from the source I got a problem for some plot
functions (pairs()) which
are used in SpikeOMatic to generate Wilson plots. It turned out that
my Linux distribution (Mandriva
10.2) does not have by default some
Xfree86 fonts: Xfree86-100dpi-fonts. The problem was
solved by installing them.
The library
You will first need to install the
Gnu Scientific Library (GSL) and the GNU
Gengetopt program. Then you need to download
the source
package. To gunzip and de-tar it type the following command:
- tar -xvzf SpikeOMaticLibrary.tar.gz
Move to the created folder (SpikeOMaticLibrary). Check out
the README and INSTALL files. If necessary edit the
Makefile (don't worry it is not complicated). In any case
calling:
should run the compilation smoothly with gcc. If you have the
GNU package plotutils installed you can then call:
If you don't have it installed just call:
Fine, to install the library (libsoml.a), the header files
(soml.h and soml_private.h)
and the executable binary (som_mcmc), type:
That's it.
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