[Bioperl-l] bioperl-1.4 ppm package for Windows

Fri Feb 27 12:20:52 EST 2004

At 09:57 AM 2/27/2004, you wrote:
>Chris,
>
>I'd always intended to have a double-boot Windows/Linux machine but I
>thought I'd check out Cygwin, just for fun. I was so impressed with it
>running Bioperl that I decided not to install Linux.

I originally installed Linux as a means to an end (using software that 
aren't Windows friendly, like mfold).  It's hard to let go of the luxuries 
of Windows, thought, especially when you have programs like Office, 
SigmaPlot, and others which make benchwork research so much easier (and 
require little to no programming experience).  I really like Linux from a 
number of aspects (open-source, development, etc).  However, I think that 
Apple has really hit upon something with OS X.  It is a nice combination of 
open- and closed-source (I don't mind paying for software,as long as it's 
reasonable) and isn't unreasonably priced.  I get the best of both worlds 
(closed source software like Office, Endnotes, etc. with open-source 
software like MySQL and Apache, with a UNIX-based OS, and nice development 
tools).  Apple also is really pushing the bioinformatics angle.  The 
constant updates for both OS X and Linux make both much more appealing to me.

That's it, my next system is a G5!!!!  Now I'll just have to sell the car...

>I must use Windows at work so pure Unix is not an option for me. Someone
>recently showed me Windows on a Linux machine running VMWare, that was
>impressive.

I have managed to get a few things running under Wine (Windows emulation in 
Linux).  It works for certain things, but I haven't tried it out too much 
b/c I have a dual-boot system.  I just get tired of the an number of 
Windows issues (I use Sun's Java VM and it crawls on Windows XP but flies 
on Linux).

Chris

>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 Chris Fields
>Sent: Friday, February 27, 2004 10:47 AM
>To: bioperl-l at bioperl.org; Lincoln Stein
>Cc: bioperl-l at bioperl.org
>Subject: Re: [Bioperl-l] bioperl-1.4 ppm package for Windows
>
>I already have it installed an it seems to be fine.
>
>I have just one question (and I don't want to start a flame war): what OS
>do you find that Bioperl works best for?  I'm using a duel-boot system with
>Windows XP and Fedora Core 1, and I've had fewer problems with Fedora (esp.
>when using GBrowse), but I don't know if this is due to the configuration
>of Bioperl, GBrowse, or Perl on either OS.  I'm considering going pure
>Linux within the year (although Mac OS X is looking very appealing).
>
>Chris
>
>At 08:45 AM 2/27/2004, Lincoln Stein wrote:
> >-----BEGIN PGP SIGNED MESSAGE-----
> >Hash: SHA1
> >
> >Hi Chris,
> >
> >Do you want to try the bioperl-1.4 ppm located on this repository?
> >
> >         http://www.gmod.org/ggb/ppm
> >
> >I put it together myself and it's the one that seems to work properly
> >for me.
> >
> >Lincoln
> >
> >On Wednesday 25 February 2004 07:26 pm, Chris Fields wrote:
> > >  I was unable to get the PPM package for 1.4 working for Windows
> > > from http:/bioperl.org/DIST and had to perform a workaround.  I
> > > decided to post it in case others were running into problems.
> > >
> > >  When I first tried installing Bioperl using PPM, it installs
> > > bioperl 1.2 first (!?!), then allows upgrading to 1.2.3.  However,
> > > it will not install 1.4 b/c of the additional dependencies
> > > (HTML-Entities and IO-Scalar).  The latter dependencies are notably
> > > not req'd for 1.2 or 1.2.3.  IMHO, I'm guessing that PPM can't find
> > > these modules b/c it is looking for specific ppm packages named
> > > HTML-Entities and IO-Scalar, not for the modules named
> > > HTML-Entities and IO-Scalar (which are included in the packages
> > > HTML-Parser and IO-stringy).  This problem could be linked to the
> > > version of PPM I'm using (3.1) on ActivePerl 5.8.3-809, both of
> > > which are very new, so I have no idea if this is a problem with
> > > older versions of PPM.
> > >
> > >  The workaround was to remove the dependencies manually.  I
> > > downloaded the relevant ppm tar file and corresponding ppd files
> > > (bioperl-1.4-ppm.tar.gz and Bioperl-1.4.ppd, respectively) to a
> > > local directory (C:\Perl\Bioperl).  Using a text editor, I removed
> > > all references to the added dependencies and saved the file.  More
> > > specifically, I deleted the following lines, listed twice under
> > > Implementations (so delete both sets!):
> > >
> > >
> > > <DEPENDENCY NAME="HTML-Entities"
> > > VERSION="0,0,0,0" />
> > > <DEPENDENCY NAME="IO-Scalar" VERSION="0,0,0,0"
> > > />
> > >
> > >
> > > I then entered PPM, set up a local ppd repository:
> > >
> > >  rep add local_bio "C:/Perl/Bioperl"
> > >
> > >  I then searched for and installed the modifed PPM file and it
> > > worked.
> > >
> > >  Like I said, I don't know if this is a PPM issue or not.  However,
> > > I think it might be a good idea to remove those dependencies just
> > > in case, as they are a bit redundant (both HTML-Parser and
> > > IO-stringy are already listed).
> > >
> > >  My two cents...
> > >  __________________________________
> > >
> > >
> > >
> > > Chris Fields - Postdoctoral Researcher
> > >  Lab of Dr. Robert Switzer
> > >
> > >  Address:
> > >
> > >  University of Illinois at Urbana-Champaign
> > >  Dept. of Biochemistry - 323 RAL
> > >  600 S. Mathews Ave.
> > >  Urbana, IL 61801
> > >
> > >  Phone : (217) 333-7098
> > >  Fax : (217) 244-5858
> >
> >- --
> >Lincoln D. Stein
> >Cold Spring Harbor Laboratory
> >1 Bungtown Road
> >Cold Spring Harbor, NY 11724
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> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>__________________________________
>
>Chris Fields - Postdoctoral Researcher
>Lab of Dr. Robert Switzer
>
>Address:
>
>University of Illinois at Urbana-Champaign
>Dept. of Biochemistry - 323 RAL
>600 S. Mathews Ave.
>Urbana, IL 61801
>
>Phone : (217) 333-7098
>Fax : (217) 244-5858
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l

__________________________________

Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer

Address:

University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
600 S. Mathews Ave.
Urbana, IL 61801

Phone : (217) 333-7098
Fax : (217) 244-5858 