$Id$


o Version

 This is Bioperl-run version 1.2.2., a stable bug fix release

o Description 
 
 bioperl-run contain modules that provides a PERL interface to various
 bioinformatics applications. This allows various applications to be
 used with common bioperl objects.

 See the Changes file for more information about what is contained in
 here.


o Installation

 You need to have the core bioperl installation before using
 bioperl-run. Select a bioperl distribution with the same release
 version.

 The installation of this package is identical to the core bioperl
 install.

 Essentially

   % perl Makefile.PL
   % make

   % make test (some tests may not succeed if you do not have the
                necessary programs or env variables defined)
   % su
   # make install


o Environmental variables

 Some important environment variables you need to be aware of.

 Variable		Values     Comment
 --------------------------------------------------------------------
 PHYLIPVERSION		3.5, 3.6   If you want to run Phylip3.6 you 
 				   Need to set this env variable to 3.6

 BLASTDIR		DIR PATH   Point to the directory where BLAST 
 	                           is installed

 GENSCAN_DIR		DIR PATH   Point to the directory where 
                                    HumanIso.smat file is installed

 EPONINEDIR          	DIR PATH   Point to the directory where 
                                    eponine_scan.jar is installed