[Bioperl-guts-l] bioperl-run/Bio/Tools/Run RepeatMasker.pm, 1.25, 1.26

Senduran Balasubramaniam sendu at dev.open-bio.org
Tue Jan 2 11:24:18 EST 2007


Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run
In directory dev.open-bio.org:/tmp/cvs-serv4539/Bio/Tools/Run

Modified Files:
	RepeatMasker.pm 
Log Message:
doc clarification, update

Index: RepeatMasker.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/RepeatMasker.pm,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** RepeatMasker.pm	4 Jul 2006 22:23:31 -0000	1.25
--- RepeatMasker.pm	2 Jan 2007 16:24:16 -0000	1.26
***************
*** 37,44 ****
  =head1 DESCRIPTION
  
! RepeatMasker is a program that screens DNA sequences for interspersed
  repeats known to exist in mammalian genomes as well as for low
  complexity DNA sequences. For more information, on the program and its
! usage, please refer to http://repeatmasker.genome.washington.edu/.
  
  =head1 FEEDBACK
--- 37,65 ----
  =head1 DESCRIPTION
  
! To use this module, the RepeatMasker program (and probably database) must be
! installed. RepeatMasker is a program that screens DNA sequences for interspersed
  repeats known to exist in mammalian genomes as well as for low
  complexity DNA sequences. For more information, on the program and its
! usage, please refer to http://www.repeatmasker.org/.
! 
! Having installed RepeatMasker, you must let Bioperl know where it is.
! This can be done in (at least) three ways:
! 
!  1. Make sure the RepeatMasker executable is in your path.
!  2. Define an environmental variable REPEATMASKERDIR which is a 
!     directory which contains the RepeatMasker executable:
!     In bash:
! 
!     export REPEATMASKERDIR=/home/username/RepeatMasker/
! 
!     In csh/tcsh:
! 
!     setenv REPEATMASKERDIR /home/username/RepeatMasker/
! 
!  3. Include a definition of an environmental variable REPEATMASKERDIR in
!     every script that will use this RepeatMasker wrapper module, e.g.:
! 
!     BEGIN { $ENV{REPEATMASKERDIR} = '/home/username/RepeatMasker/' }
!     use Bio::Tools::Run::RepeatMasker;
  
  =head1 FEEDBACK



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