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INSTALL
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INSTALL
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FFP 3.18 - Feature Frequency Profile Phylogenetics Package
Feb 20, 2012
Author: Gregory E. Sims
This is a collection of programs for implementing the FFP
(Feature Frequency Profiles) method of phylogenetic comparison.
The FFP utilities can be installed using the tradition syntax
./configure
By default the executables will be installed in /usr/bin.
To change this location or if you are not the superuser
(i.e. do not have root access), you can do this by specifying
the install directory:
./configure --prefix=/home/yourname/dir
Make sure to add the /home/yourname/dir/bin to your PATH
variable.
To compile:
make
To check the installation:
make check
All tests should pass. If they do not please contact gesims@lbl.gov,
and report which tests have failed with information about your
system such as the operating system and CPU type.
To install:
make install
To use the ffpgui interface you will need to have the perl/tk
module installed. The most efficient way to do this on a linux
machine is to use the perl CPAN shell.
perl -MCPAN -e 'shell'
cpan> install Tk
Use --disable-gui to bypass installation of the ffpgui interface.
The ffpgui system is still in beta form (i.e. experimental). It will
not function properly in Cygwin IF you install the perl/Tk package
automatically via the cygwin setup.exe. You must compile from source
using 804.029 which can be checked out using svn (aka. subversion):
svn checkout https://svn.perl.org/modules/Tk/trunk
cd trunk
perl Makefile.PL x # Don't forget the x!
make
make install
Hopefully sometime soon 804.029 will be placed on CPAN, and replace
804.027.
You will also need to install the X11 X windows libraries for
Cygwin via setup.exe. Before running ffpgui, You will need to
start an x-windows session, via 'startxwin'.
However any native linux X-windowing system will be able to use
ffpgui without issue, provided you are using a system with X11
enabled. If running on your local machine there should be no
issue, but if running on a remote host then you will need to have
your DISPLAY variable set (in your shell's rc file, for example
.bashrc), and you should log in to the remote system with the -Y
option (enable X11 forwarding).
#Enable X11
export DISPLAY=:0.0
#Enable X11 forwarding
ssh -Y user@remotehost.com
To see examples of how to use the FFP programs see the README
file, or the doc/tutorial.pdf file.
There is a full collection of man files which are placed in
your system's man directories upon install. If you have used
the --prefix option you will need to update $MANDIR to specify
the proper path for man to search for the manual files.
In the doc/ subdirectory the manuals have been compiled into
PDF form for quick reference. There is also a quick start tutorial
located in the doc/ subdirectory. Upon install these are placed
in /usr/local/shared/doc/ffp or PREFIX/shared/doc/ffp (if you have
used --prefix during configuration).
Finally there are some examples of trees used in publications
supplied in the examples/ directory. Upon install these are
placed in /usr/local/shared/examples/ffp or PREFIX/shared/doc/ffp.
**** Common Error messages during compilation:
troff: fatal error: can't find macro file s
You likely do not have a full install of the groff package.
To build the tutorial files using the Manuscript macro set,
you'll need to update your install of groff. We have seen
this error on the Ubuntu 11.10 system. You will need to install
groff. Try:
sudo apt-get install groff
which will give you access to full set of macros.
Perl module Tk missing. Install using: perl -MCPAN -e 'install Tk'.
Or use configure with '--disable-gui' to disable ffpgui build.
There are two solutions. Install the required perl module.
Or disable gui compilations during the install. Add the
--disable-gui flag to the configure invocation:
./configure --disable-gui
and then compile as normal.
(C) 2009-2012
gsims1997@yahoo.com