[Bioperl-l] Windows Testing

[Paul Boutros]

I looked into the point made by Pierre Far about the current Windows ppm
install routine not working with PERL 5.8.0.  I updated the text below to
take that into account.

Also, on a more general note, am I mistaken in noting that the ppm install
of Bioperl doesn't include these directories?
/test
/doc
/examples
/models
/scripts
/t

=========================================================================
BioPerl on Windows
==================

1.0 Installation
1.1 PERL on Windows
1.2 External Modules
1.3 Installing Bioperl
1.3.1 ActiveState for PERL 5.6.1
1.3.2 ActiveState for PERL 5.8.0
1.3.3 Download Archive
1.3.4 If All Else Fails...
2.0 Windows Specific Behaviour
2.1 Subroutine <name> redefined at location <location> warnings
2.2 Consed

1.0 Installation
================

Windows installation of BioPerl requires three steps:
i)   installation of PERL
ii)  installation of external modules
iii) installation of BioPerl itself

I'll quickly summarize my findings on each of those below.

1.1 PERL on Windows
===================

There are lots of ways of installing PERL on a Windows machine.  Probably
the easiest and most common is to get the most recent build from
ActiveState.  You can also build PERL yourself (which requires a C
compiler) or download one of the other binary distributions.  Regardless
of which way you choose to go, if have a functioning PERL build higher
than version 5 or so you can procede to the next step.

The PERL source for building it yourself is available from CPAN
(http://www.cpan.org), as are a few binary distributions.

ActiveState is a software company (http://www.activestate.com) that
provides free builds of PERL for windows users.  They are currently
(December 2002) providing a very stable build of PERL 5.6.1 while a beta
version of PERL 5.8.0 is also available.  I suggest that you stick to the
production version of 5.6.1 because: a) it is easier to install the
external modules for 5.6.1 and b) I find 5.8.0 beta a bit unstable at the
moment.

1.2 External Modules
====================

The installation documents supply a very comprehensive list of external
dependencies (i.e. see http://www.bioperl.org/Core/external.shtml).  You
do not need to install external modules for the parts of BioPerl that you
do not intend using.  That being said, if you don't know what to install,
try to install all externals.

If you are using ActiveState, I recommend first attempting to download
your external modules via the ActiveState Perl Package Manager (PPM).  To
use it, just go to a command-prompt and type ppm while connected to the
internet.  The software will connect to a repository of available modules
that you can install.  For example, to install IO::String you would type:
"install IO::String"

If you are using ActiveState 5.8.0, you will find that some external
modules are not yet available via ppm.  In that case you will have to
download them directly from cpan (http://www.cpan.org) and follow the
specific build procedures for each module.  This is one major reason for
avoiding the ActiveState 5.8.0 beta version.

1.3 Installing BioPerl
======================

You have two main choices for installing BioPerl.  If you are using
ActiveState you can use ppm to install with the commands:

1.3.1 ActiveState For PERL 5.6.1
================================

PPM> set repository bioperl http://bioperl.org/DIST/
PPM> search bioperl             (shows available bioperl versions)
PPM> install bioperl		(will install the default version)

1.3.2 ActiveState For PERL 5.8.0
================================

ppm> repository add bioperl http://bioperl.org/DIST
ppm> search bioperl		(shows available bioperl versions)

This last command returns a numbered list of the available bioperl
versions.
Select the number of the version you wish to install and type:

ppm> install <number>

1.3.3 Download Archive
======================

You can download BioPerl as a compressed archive from:
http://www.bioperl.org/Core/Latest/index.shtml
This archive can be uncompressed with WinZip (or most other Zip
utilities).

Don't worry if you get a warning saying something like "Archive contains
only one file!  Extract and decompress?".  This is just a variation in how
UNIX and Windows software likes to compress files.  Choose yes, and all
will be well.

You will need access to a make utility to utilize this approach.

1.3.4. If All Else Fails....
============================

The BioPerl directory tree should be extracted intact (i.e. ensure "Use
Folder Names" is selected in WinZip) and must be placed so that it is in
your @INC path.  It may be easier to extract the directory tree to another
location and moving the \Bio directory to \perl\site\lib

This approach will not install compiled versions of any modules in the
package, and isn't recommended.

1.4 Testing Installation
========================

It is possible to test your BioPerl installation on windows with "make
test", although this requires having a copy of make utility available on
your system.  If you used ppm to install, this step will not be possible
as activestate doesn't install this information.

2.0 Windows-Specific Behaviour
==============================

Items of windows-specific behaviour are listed below.

2.1 Subroutine <name> redefined at <location> Warnings
======================================================

BioPerl does not get along particularly nicely with the PERL -w flag on
windows systems.  The sample script below shows what happens with many
scripts:

test.pl
###############################################
use Bio::ClusterIO;
my $stream = Bio::ClusterIO->new(
		'-file'		=> $ARGV[0],
		'-format'	=> 'UniGene',
		);
###############################################

c:\> perl -w test.pl Hs.Data
Subroutine new redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line
222.
Subroutine unigene_id redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm
line 284.
Subroutine title redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line
306.
Subroutine gene redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line
327.
Subroutine cytoband redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm
line 345.
Subroutine mgi redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line
362.
Subroutine locuslink redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm
line 390.
Subroutine gnm_terminus redefined at
C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 420.
Subroutine scount redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm
line 436.
<and many more like this>

These warnings messages are basically the result of the windows version of
PERL being more cautious than other versions.  These are only warnings
messages, and can safely be ignored.  For production code, you can remove
the -w flag and you will not receive these warnings.

2.2 Consed
==========
The consed module cannot be run under Windows.
=========================================================================