bioperl-run for Debian
----------------------

(Extracted from the INSTALL file)

ENVIRONMENT 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
                           
 PAMLDIR        DIR PATH   Point to directory where PAML is 
                           installed

Generally the all-caps program name concatenated to 'DIR' patten for
environment variable names is followed for most programs. However
there are some exceptions (some require an underscore between the
program name and 'DIR'), so check the documentation for the module
you're interested in using.

Note that for some programs, having the executables in your path is
not enough - the correct environment variable still needs to be set,
and sometimes it shouldn't point to the executable location, but
somewhere else - again, check the documentation.