[Bioperl-l] Problems installing Bio::DB
cjfields at uiuc.edu
Tue Oct 26 11:08:00 EDT 2004
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?
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
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
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
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:
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
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
>>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?
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Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer
University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
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Phone : (217) 333-7098
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