Skip to content
This repository


Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP

BioPerl wrappers

Fetching latest commit…

Cannot retrieve the latest commit at this time


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

Something went wrong with that request. Please try again.