[Bioperl-l] (no subject)

Chris Fields cjfields at uiuc.edu
Thu Oct 28 10:53:56 EDT 2004

For some reason I didn't see this pop up on the weblist, so I'm sending it 

At 01:11 AM 10/26/2004, you wrote:
>Sorry I can't help here since I've never tried to install bioperl-db on 
>Windows. Can anyone out there who is on the same platform help?
>         -hilmar

I have installed bioperl-db on Windows XP without a problem (although I 
plan on switching over to MacOSX within a year!).  Basically, here's  what 
I did:

1)  Install Activestate's free Perl package (the latest version of Perl 5.8).
2)  Using PPM, install Bioperl.  There are installation instructions for 
this on the website, and I think Sudha has progressed at least this far.
3)  Install your database of choice.  I installed MySQL (which has a 
Windows installer).
4)  Install the database interface modules (DBI and DBD-MySQL, both 
available through PPM).  Adding Randy Kobe's repository in PPM helps here, 
although it isn't necessary (it does help if you want other modules for 
bioperl, like GD).
5)  Get BioSQL schema.  Judging by the error, you may be missing this or 
bioperl-db (which operates with BioSQL).
         a)  Go to the CVS repository and download the bioperl-db package 
as tarball.
         b)  Decompress the tarball and view the installation 
instructions.  This will tell you where to get BioSQL (hint: it's in the 
same CVS repository as well as the CVS mentioned in the installation files).
         c)  Get the particular schema for your database.  This is located in


6)  Install bioperl-db using nmake.  This worked well for me, although 
nmake is notoriously buggy sometimes.
         a)  Using a shell (or command prompt for Windows users), migrate 
to the bioperl-db folder (which you decompressed above).
         b)  Type the following:

                 perl Makefile.PL
                 nmake install

         c)  You might get some errors here with nmake.  Don't panic (and 
remember your towel).  Okay, bad Douglas Adams humor...
         d)  You don't have nmake?!?  get the old nmake here:


         e)  nmake also comes with MSVC++.  You don't have MSVC++?!?  Don't 
panic yet, because...
         f)   I've heard reports that make also works (using MinGW or other 
windows-ported tools), but I haven't tried these, so be warned.
7)  create you database.

         mysqladmin -u root create bioseqdb

8)  load the schema into your database.

mysql -u root bioseqdb < biosqldb-mysql.sql

9)  load the taxonomy database if needed (I think it's recommended).  The 
script is in the

biosql-schema/scripts folder.

Anything I'm missing?  I think I've listed almost everything.  I do think 
Cygwin is a good alternative (the installation is exactly like the 


>On Wednesday, October 20, 2004, at 08:03  PM, Sudha S wrote:
>>I have been trying to install the Bio::DB for a week
>>now and I need some help in this badly.
>>I keep getting the error :
>>'Error: no suitable installation target found for
>>package bioperl-db.'
>>I remember that i was prompted to give path for
>>/usr/lib directory and I do not have this folder on my
>>machine which is running Windows XP. What should be
>>done to get over this problem?
>>Thank you,
>>Do you Yahoo!?
>>Declare Yourself - Register online to vote today!
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>Hilmar Lapp                            email: lapp at gnf.org
>GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org


Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer


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  

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