/usr/share/doc/bioperl-run/README.Debian is in bioperl-run 1.6.9-1.
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(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.
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