[Bioperl-l] Windows Testing

[Paul Boutros]

On December 10th, 2002 Ewan Birney Wrote:

> Also - Paul - is there any chance of you writing up a HowTo on
> installing on windows so we can put that into the documentation of
> bioperl - would help alot of people.
> 
> If we need to we can reassure people about warnings in the test suite or
> other things (eg, function redefined warnings) there...

Okay, here's a stab at it: not sure if this is what you had in mind. 
Corrections or suggestions welcome.

Incidentally, there is a similar (but a little old) document at:
http://bioperl.org/Core/windows-bioperl.html

Paul

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

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 BioPerl
===========

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

PPM> set repository bioperl http://bioperl.org/DIST/
PPM> search bioperl             (this will show you what are the available
bioperl versions)
PPM> install bioperl		(will install the default version)

Alternately, 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.

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

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 use ActiveState and the ppm to install BioPerl this
step is definitely unnecessary and can usually be skipped in other cases.


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.
=========================================================================