[Bioperl-l] Blast returns result, but does not return hits

Chris Fields cjfields at uiuc.edu
Wed Feb 22 19:02:38 EST 2006


> 
> I am using ActivePerl 5.8.7 downloaded from
> activeperl.com. I just happened to install it under
> c:\mod_perl\Perl directory (application has hardcoded
> dependencies for this directory). I am not using
> apache/mod_perl/perl.
> 
> Please see below version string returned by perl
> exectutable.
> 
> 
> C:\bioperl-live\bioperl-live>perl -version
> 
> This is perl, v5.8.7 built for
> MSWin32-x86-multi-thread
> (with 14 registered patches, see perl -V for more
> detail)
> 
> Copyright 1987-2005, Larry Wall
> 
> Binary build 815 [211909] provided by ActiveState
> http://www.ActiveState.com
> ActiveState is a division of Sophos.
> Built Nov  2 2005 08:44:52
 
When you type 'perl -V' what do you see (make sure it is a capital 'V', not
lower case).

> http://perl.apache.org/docs/2.0/os/win32/install.html
> >
> > The only Perl for Windows we have actively supported
> > is ActivePerl AFAIK,
> > but maybe we can walk through this.  Anything
> > learned here can be added to
> > the installation instructions in case this comes up
> > again.
> >
> I used 'ppm' to install packages (DBI, Oracle-DBD,
> bioperl etc) before, so this is the first time I tried
> to install it using 'nmake' utility.
>
> After downloading the latest bioperl tar ball and
> replacing the blast.pm file, can I just do ppm install
> bioperl instead of doing nmake?

Okay, so I know you're using PPM now.  No, you can't do that.  I'm adding a
section to this page:

http://bioperl.open-bio.org/wiki/Making_a_BioPerl_release

about building your own PPM; it will explain everything.  It isn't up yet
but should be up tonight or tomorrow.  BTW, you'll still need nmake to work
for this to work.  Again, make sure nmake is in your PATH env variable, or
at least have it in the same directory you plan running 'nmake', 'nmake
install.'  Although nmake is buggy I haven't had a problem with it yet.
 
> > Next: you obviously have installed Bioperl before
> > (v1.2.3); did you use
> > 'make' or 'nmake', or was it from a repository (like
> > IndigoPerl's GPM)?
> > AFAIK, you would install it like you would any other
> > perl module; there
> > should be no problem with 'make/nmake', though
> > 'make/nmake test' will not
> > pass completely (it should pass most tests, though,
> > otherwise something is
> > seriously wrong).
> >
> > The other option, though not as nice, is setting the
> > PERL5LIB variable to
> > include the bioperl-live directory; it works for me
> > while I'm developing.
> 
> I tried setting PERL5LIB, but it did not make any
> difference. I am still getting the same errors.
 
Do you mean the errors from nmake or errors from your scripts?  If PERL5LIB
is set properly then it should parse those directories for modules before it
checks the rest in @INC (i.e. will not need to make and install these using
nmake).  

The reason I don't recommend this is it's not the best habit to get into
installing the entire Bioperl distribution into a folder and using PERL5LIB,
but some are forced to do it this way, so it's there if you need it.  A
direct installation is recommended if possible.

The PERL5LIB I use below only contains modules I'm working on or
modifications of current modules (like SearchIO::blast, RemoteBlast, etc).
Bioperl from CVS is installed via PPM (custom-built PPM, BTW, using the
instructions I mentioned).  

The following is what my PERL5LIB is set to.  Note that it also tells you
what @INC is set to as well:

C:\Perl\src\bioperl\bioperl-live>perl -V
Summary of my perl5 (revision 5 version 8 subversion 7) configuration:
  Platform:
    osname=MSWin32, osvers=5.0, archname=MSWin32-x86-multi-thread
    uname=''
    config_args='undef'
    hint=recommended, useposix=true, d_sigaction=undef
    usethreads=define use5005threads=undef useithreads=define 

<blah blah blah>

  Compiled at Nov  2 2005 08:44:52
  %ENV:
    PERL5LIB="C:/Perl/src/bioperl/bioperl-live;
C:/Perl/src/bioperl/bioperl-db"
  @INC:
    C:/Perl/src/bioperl/bioperl-live
     C:/Perl/src/bioperl/bioperl-db
    C:/Perl/lib
    C:/Perl/site/lib
    .



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