[Bioperl-l] Questions on module installation

Li, Qingqin [PRDUS] QLi2 at prdus.jnj.com
Thu Jul 10 17:42:59 EDT 2003

Dear All,

Finally I came to this group seeking for advice. I poked it a little bit in
the The Bioperl-l Archives and did not find an easy way of searching the
entire archives except by month. I was hoping to find the answer from
previous posting and not to annoy anyone if the topic was discussed before.
Anyway, here it goes.
I was using an old version (June 2001) of Bio::Tools::Blast module to parse
my blast report. I found that if I set -signif=>'1e-100', the parser could
not handle score above e+04 consistently. It thinks there is no significant
hit in the following case. 
For example

Sequences producing significant alignments:
Score (bits) 	E Value
 ENST00000006659 Gene:ENSG00000006283 Clone:AC004590 Contig:AC004...
1.206e+04 	0.0 

I thought perhaps the problem has been fixed in the newer version of
Bio::Tools::Blast parser, only to find out that this method in the later
version of BioPerl has been deprecated. 
Therefore I decided to install an version of bioperl for myself. This leads
me to the second question that I have been puzzled for a long time. It is
related to installing perl modules in a personal directory, since I do not
have system privilege.
In the past I had set PERL5LIB environment variable to include some of my
local perl modules so that I do not to say use lib "xxx". I also tried to
install perl 5.8 before perhaps in my home directory (don't quite remember
this point? I deleted the installation later on. Guessed from the error
message below). Currently, if I use
perl Makefile.PL PREFIX=/my/personal/perl 

I got an error message saying
Unable to locate installed Perl libraries or perl source code.
You got this message because MakeMaker could not find

If I set PERL5LIB to null, I don't get the above error message, but at the
same time, perl does not know of the local modules I have installed (modules
that bioperl depends on, for example). Why this behavior happen? Is there a
fix for it? Is it because of the uninstall of local perl is not clean?

If I disregards the complaint of missing modules that bioperl1.2.2 is
depending on, and continue with "make"

I got an 

** Termination code 138 (bu21)

error. I could still install some simple module such as MIME::LITE in
/my/personal/perl directory (under the mode of NULL PERL5LIB).

I am using a irix UNIX (SGI). Any insights into these problems will be
greatly appreciated.


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