[Bioperl-l] RE installing bioperl in windows

[Pablo Marin Garcia]

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 
active-state.

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:

http://search.cpan.org/src/JWIED/DBD-mysql-2.1025/INSTALL.html#windows/cygwin.


-- 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 -> 
problems
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
 
-- EMACS

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 
in
> the Unix environment so the approach that's easiest for me is to use 
Bioperl
> with Cygwin, which is a free Unix emulator for Windows. So step 1 would 
be
> to install Cygwin (www.cygwin.com) along with the Cygwin packages 
binutil,
> gcc, make, and perl. When Cygwin is installed you want to start it up 
and
> install Bioperl just as you would in Unix. These steps are described in 
the
> INSTALL document, take a look at the sections THE BIOPERL BUNDLE and
> INSTALLING BIOPERL THE EASY WAY USING CPAN
> (http://bioperl.org/Core/Latest/INSTALL). When you first start using 
CPAN in
> Perl it will need some configuration, answering all of its questions 
with
> 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 
your
> system or your existing files in any way, it doesn't create partitions, 
it
> 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 
install.
>> 
>> Thank You
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-------------------------------------------------
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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

www.ebi.ac.uk/Information/Staff/pablo_marin.html
www.ebi.ac.uk/~dysdera/

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