# $Id: INSTALL 15578 2009-02-26 02:17:03Z bosborne $

bioperl-run INSTALLATION

INSTALL THE RIGHT BIOPERL

You need at least the corresponding version of Bioperl. Since this
is BioPerl-run 1.6.1, you should use BioPerl 1.6.


INSTALLATION

Installation instructions at the following address apply here:
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
The next 2 sections summarize the essential points from there.


CPAN INSTALLATION

To install using CPAN you will need a recent version (v1.8802 has
been tested) of it and your prefer_installer conf set to 'MB':

  >cpan
  cpan>o conf prefer_installer MB
  cpan>o conf commit
  cpan>q

Find the name of the bioperl-run version you want:

  >cpan
  cpan>d /bioperl-run/
  Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
  Distribution C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
  
Now install:

 cpan>install C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz

If you've installed everything perfectly then you may pass all the tests
run in the './Build test' phase.

It's also possible that you may fail some tests. Possible explanations:
problems with local Perl installation, previously undetected bug in
Bioperl, flawed test script and so on. A few failed tests may not affect
your usage of bioperl-run.

If you decide that the failed tests will not affect how you intend to use
bioperl-run and you'd like to install anyway do:

 cpan>force install C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz

This is what most experienced Bioperl users would do. However, if you're
concerned about a failed test and need assistance or advice then contact
bioperl-l@bioperl.org.

MANUAL INSTALLATION

Download the bioperl-run archive, then extract its contents. Example:

  >gunzip bioperl-run-<release-version>.tar.gz
  >tar xvf bioperl-run-<release-version>.tar
  >cd bioperl-run

where <release-version> is the current release.

Issue the following command from within bioperl-run/:

  >perl Build.PL

You can run regression tests and install bioperl-run using the
following commands:

  >./Build test  
  >./Build install

NOTE: many tests will be skipped without the necessary environment
variables set to tell Bioperl where your programs are installed.

INSTALLING bioperl-run ON WINDOWS

The following page on the BioPerl website has up-to-date
instructions on how to install bioperl-run on Windows:

http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows

(the instructions are aimed at bioperl-core, but apply
equally to bioperl-run)


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.