[Bioperl-l] This may help someone install bioperl

[Pierre Far]

Greetings!

I just had to hack/work around some silly bugs and inconsistencies. Here is 
an account of the problem (so that it may be fixed hopefully) and a working 
solution (I just did it).

The setup:
Windows XP machine, no service packs or anything (fresh install).
Downloaded and installed ActiveState Perl. Filename: 
ActivePerl-5.8.0.804-MSWin32-x86.msi

The Problem:
To install Bioperl, I read the install file that came with the downloaded 
version. It said that the ActiveState Perl there is a package manager (true) 
that can be used to install bioperl. I thought I would try that.

The first problem is that ActiveState distributes 2 package managers - PPM3 
and PPM2. PPM3 is the default, and is newer and the syntax is different from 
PPM2. The instructions stated in the install file are for PPM2. A quick look 
in the HTML docs that come with Perl confirms that. So the first obstacle is 
overcome by typing ppm2.bat at the command line instead of just "ppm". 
Further, PPM3 has a bug in it at line 174 in Repository.pm and crashes when 
you try to use it.

Once that worked, I set up the repository as described in the install file 
as follows:

set repository bioperl http://bioperl.org/DIST/

That worked. Then I searched for bioperl

search bioperl

and it returned the hits. Excellent; now we can install:

install bioperl

That seemed to work until an error got back to me saying that the package is 
not meant for this build of Perl. The stated build of Perl is

MSWin32-x86-multi-thread-5.8

So I went to http://bioperl.org/DIST/ and found the PPD files. The 
architecture names are set to

MSWin32-x86-multi-thread

Notice that this is missing a bit: the suffix "-5.8".

The Solution

To cut a long story short, the work around is as follows:

Download the PPD file for the package you want.

Edit it so that the architecture name is now the correct one.

Then to a webspace you have access to, upload the new (edited) PPD file. For 
the sake of this example, let's say you uploaded it to 
http://yahoo.com/bioperl/ .

The next step is to type ppm2.bat at the command line. Once in PPM2, set a 
new repository: set repository MyBioperl http://yahoo.com/bioperl/ .

Next search for bioperl ("search bioperl") and you should see it as a 
package from your webspace. That's good.

Install bioperl ("install bioperl") and it should work!


One extra tip: If your webspace can be accessed using virtual hosting, it 
seems that PPM2 doesn't like that. Set the repository to the full proper 
URL.

And one last problem: The bioperl-110.ppd file points to a PPM file that 
cannot be found! The codebase is set to 
http://bioperl.org/DIST/bioperl-1.1.0-ppm.tar.gz and that does not exist 
(HTTP 404 - Not found).

Hope this helps someone. Off to explore bioperl now.

Pierre Far.
--
http://ekstreme.com





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