[Bioperl-l] bioperl-run on windows XP

Brian Osborne brian_osborne at cognia.com
Wed Apr 21 08:17:07 EDT 2004

To whom it may concern,

First, it doesn’t seem that you installed the bioperl package, you’ll need
it in order to run the bioperl-run package. Second, the way that you
installed bioperl-run, extracting and copying, doesn’t resemble any of the
usual ways one would install bioperl, or perl and perl modules generally, my
guess is that it’s more-or-less guaranteed that you’ll encounter various
problems if you take this approach. I suggest that you take a look at the
INSTALL.WIN file and choose one of the approaches described there. To answer
your question, yes, you can run bioperl on XP.

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 cr cd
Sent: Tuesday, April 20, 2004 10:52 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] bioperl-run on windows XP

Hi, all:
     This is my first time post, thank you for your attention and any
suggestion is greatly appreciated.
I just wonder if all modules of bioperl-run can work properly on wondows XP
system. I tried ClustalW.pm, ProtPars.pm and ProtDist.pm. ClustalW module
works fine after I copy clustalw.exe into my working folder. But ProtPars
and ProtDist modules not work even if ProtPars.exe and ProtDist.exe works
fine in my woking folder. Any suggestions? Thank you so much.

A. Steps I took to install Bioperl-run:
1.        download bioperl-run-1.4 (current_run_stable.tar.gz)  from
2.        Copy current_run_stable.tar.gz to my folder  /bioperl_run and
this gz file.
3.        Copy    \bioperl_run\bioperl-run-1.4\Bio\Tools\Run (folder) to
C:\Perl\site\lib\Bio\Tools and replace the old folder Run, so that in
current Run folder there are many new modules that I wish to use such as
B. My code:
use Bio::Tools::Run::Phylo::Phylip::ProtPars;
my $tree_factory =
my $tree = $tree_factory->run("./folder/file.phy");
C. Error message:
'protpars.exe' is not recognized as an internal or external command,
operable program or batch file.
------------- EXCEPTION  -------------
MSG: Protpars did not create treefile correctly
STACK Bio::Tools::Run::Phylo::Phylip::ProtPars::_run
STACK Bio::Tools::Run::Phylo::Phylip::ProtPars::run
STACK toplevel Align_from_db.pl:169

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