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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
o Installation
You need to have the core bioperl installation before using
bioperl-run. Select a bioperl distribution with the same release
The installation of this package is identical to the core bioperl
% 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
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