bioperl-run INSTALLATION

INSTALL THE RIGHT BIOPERL

You need at least the corresponding version of Bioperl. Since this
is BioPerl-run 1.007001, you should use BioPerl 1.007001.


INSTALLATION

Installation instructions at the following address apply here:
http://bioperl.org/INSTALL.html
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 CJFIELDS/BioPerl-Run-1.007001.tar.gz

Now install:

 cpan>install CJFIELDS/BioPerl-Run-1.007001.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 CJFIELDS/BioPerl-Run-1.007001.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)