[Bioperl-l] RE installing bioperl in windows

Brian Osborne brian_osborne at cognia.com
Wed Jun 30 09:10:16 EDT 2004


My first guess if someone had trouble connecting to Mysql in the
Cygwin/Windows world would be that something's wrong with the connection
string. Did you try something like this?

use DBI;
use CGI;
use CGI::Carp qw(fatalsToBrowser);


my $dsn = "DBI:$driver:database=$db:host=";
my $dbh = DBI->connect($dsn,$user,$passw) or croak "Error connecting :" .

$driver is "mysql", of course, local Mysql database, Apache provided by

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Pablo Marin
Sent: Tuesday, June 29, 2004 3:15 PM
To: bioperl-l at portal.open-bio.org
Cc: habulleef at kfshrc.edu.sa
Subject: [Bioperl-l] RE installing bioperl in windows

Hello Hana,

Yes, the best option is intall cygwin that includes perl 5.8,
and you have more modules (from CPAN) that the ones provides by ppm from

Just in case it would be usefull for someone, these are the issues about
the integration of cygwin perl and windows, that I have found:

-- mysql:

Until recently I have been using the windows perl because I was unable to
install DBD::mysql in the cygwin perl.

But now following this instruction all works ok:


-- CGI

Another thing to do is to map the cygwin perl.exe to the IIS (if you
want to run cgis) [I tried first use with apache but I had failed ->
to conect to mysql through cgi, probably permision problems]

IIS -> map the extensions of the perl scripts to perl ->
    \...\...\perl.exe %s%s  (the %s are essential) !!!!

I have both windows perl and cygwin perl ->  I have mapped the plx to
windows and the .pls to cygwn perl in the IIS


The windows emacs can be used with cygwin perl aswell: The best thing is
open windows emacs from  a cygwin console:
I have this alias in my bashrc
alias wem='/cygdrive/c/emacs-21.3/bin/runemacs.exe -bg black -fg green
-bd ForestGreen'

Then you have the bash enviromental variables in the emacs (including
PERL5LIB with the cygwin bioperl path).

Essential emacs module when debugging =>  cygwin-mount.el -> understand
cygwin paths

  Problems that I have not solved with w-emacs+cygwin-perl
     -> when using perldb, the 'n' and 's' are not repeated by default
when intro
     -> the STDOUT is buffered and only released if you print something
from the perldb.

Cygwin comes with emacs and you can run it from the shell with 'emacs -nw'
and then perldb works fine with cygwin perl.

Hope this helps

> -----Original Message-----
> From: Brian Osborne wrote
> Hana,
> How easy an approach is may depend on your background. I'm comfortable
> the Unix environment so the approach that's easiest for me is to use
> with Cygwin, which is a free Unix emulator for Windows. So step 1 would
> to install Cygwin (www.cygwin.com) along with the Cygwin packages
> gcc, make, and perl. When Cygwin is installed you want to start it up
> install Bioperl just as you would in Unix. These steps are described in
> INSTALL document, take a look at the sections THE BIOPERL BUNDLE and
> (http://bioperl.org/Core/Latest/INSTALL). When you first start using
> Perl it will need some configuration, answering all of its questions
> the default answers is usually the right thing to do.
> A note on Cygwin: it doesn't write to your Registry, it doesn't alter
> system or your existing files in any way, it doesn't create partitions,
> simply creates a cygwin directory and writes all of its files to that
> directory. To uninstall Cygwin just delete that directory.
> Brian O.
>> -----Original Message-----
>> From: bioperl-l-bounces at portal.open-bio.org
>> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of
>> habulleef at kfshrc.edu.sa
>> Sent: Tuesday, June 29, 2004 4:30 AM
>> To: bioperl-l at bioperl.org
>> Subject: [Bioperl-l] Installing Bioperl
>> Hello,
>> I am looking for an easy straight forward way to install Bioperl for
>> windows 2000
>> as have tried the steps in bioperl .org and had difficulties to
>> Thank You
.             /   __   \                      /   __   \
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'It is true that a mathematician  who is not somewhat of a poet, will
never be a perfect mathematician'
karl Weierstrass (1902)
Science is for those who learn;
poetry, for those who know.
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Pablo Marin Garcia.

E-mail address: pablo at ebi.ac.uk //  pablo.marin at uv.es

EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton


Cambs. CB10 1SD, United Kingdom
Phone: +44 (0)1223 494 478   FAX: +44 (0)1223 494 468

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