$Id$
/framework/perl
This section holds the following subdirectories:
	- cipres: perl cipres bindings (includes sdk, end user api)
	- cope: corba/perl libraries (orb, etc.)
	- phylo: perl-ish set of libraries for handling trees, taxa and matrices
	- doc: autogenerated documentation (typically this is empty, will be written to by 'perl Build html')
	- bundle: listing of prerequisites as a cpan bundle (not used from source tree, is mirrored on cpan)

Pre-built dependencies
	- for Win32, OSX-ppc (>10.3) and OSX-intel (>10.4) we provide 
	  a binary build of all prerequisites.
	- to install a prerequisite bundle:
		* set CIPRES_PERL_HOME environment variable to the perl root
		* run (sudo) "./Cipres-prereq-latest-[version].exe" (osx-ppc=5.8.1, osx-intel=5.8.6)
		* (OSX: "sudo chown `whoami` $CIPRES_PERL_HOME/bin/perl")
		* (OSX: "chmod 711 $CIPRES_PERL_HOME/bin/perl")
		* (OSX: "source $CIPRES_PERL_HOME/etc/perlvars.bashrc")
		* (Win: "%CIPRES_PERL_HOME%/etc/perlvars.bat")

	# things should work now. The following must not have "Can't find ... in @INC" errors:
	perl -MCipres::Prereq -e 1

Source dependencies
	To obtain the prerequisites from source, install Bundle::CIPRES from cpan:

	- perl -MCPAN -e 'install RVOSA/Bundle-CIPRES-0.03.tar.gz'

	If you have all prerequisites set up, please consider contributing a configured archive
	like the ones for osx intel and windows. Do this by running the 'build_deps_lib.(sh|bat)' 
	script from within /framework/perl.	

Environment variables
	- CIPRES_PERL_HOME needs to be set before anything else
	- windows variables are in %CIPRES_PERL_HOME%/etc/perlvars.bat after install
	- osx variables are in $CIPRES_PERL_HOME/etc/perlvars.bashrc after install

Installing CIPRES libraries
	- first,install Bio::Phylo:
		* 'cd phylo'
		* 'perl Build.PL'
		* 'perl Build install'
	- install the cope -->BRANCH<-- (branches/rvosa_cope_0_062/)
		* 'svn co http://nladr-cvs.sdsc.edu/svn/CIPRES/cipresdev/branches/rvosa_cope_0_062/'
		* 'cd rvosa_cope_0_062'
		* 'perl Build.PL'
		* 'perl Build install'
	- install the cipres bindings
		* 'cd cipres'
		* 'perl Build.PL'
		* 'perl Build install'