[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/959

[Jason Stajich]

On Thu, 10 May 2001 bioperl-bugs@bioperl.org wrote:

> Hi,
> 	I just installed bioperl on my local system which is running linux
> Mandrake 8.0 and has perl 5.6.0
> 
> 
> My make test returns with an error:
> 
[snip]

> 1.  I have the programs tcoffee, blast, and clustalw installed in
> /usr/local/bin.  How do I get the test script to realize this?
> 
Read the perldoc documentation for
Bio::Tools::Run::Alignment::Clustalw,
Bio::Tools::Run::Alignment::TCofee,
Bio::Tools::Run::StandAloneBlast

You need to have the following enviroment variable defined
CLUSTALDIR=path to dir containing clustal 
TCOFFEEDIR=path to dir containing tcoffee 
BLASTDIR=path to dir containing blastall,bl2seq, etc
BLASTDATADIR=path to dir containing blastable dbs
> 
> 2. I went on and installed dispite this error.  I then tried to run
> examples/standaloneblast.pl, but get the following error:
> 
you don't have the nr db installed or you do not have BLASTDATADIR env
variable defined so this will not work until then.

> [root@antigua bioperl-0.7.0]# examples/standaloneblast.pl
> Beginning MATRIX parameter-varying example...
> Performing BLAST with MATRIX = BLOSUM62
> [blastpgp] WARNING: Could not find index files for database
> /usr/local/blast/data/nr
> -------------------- EXCEPTION --------------------
> MSG: blastpgp call crashed: 256 /usr/local/blast/blastpgp -d 
> /usr/local/blast/data/nr  -i  t/cysprot1.fa  -o  /tmp/TUcbXqIeZc  -M 
> BLOSUM62
>  
> STACK Bio::Tools::Run::StandAloneBlast::_runblast
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Run/StandAloneBlast.pm:568
> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Run/StandAloneBlast.pm:540
> STACK Bio::Tools::Run::StandAloneBlast::blastpgp
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Run/StandAloneBlast.pm:478
> STACK main::vary_params examples/standaloneblast.pl:212
> STACK toplevel examples/standaloneblast.pl:91
> -------------------------------------------
> 
> I can get by this by specifying $database='../database/nr' but is there
> a better way to note that the blast programs data files may be stored in
> a different directory than the databases.  For example when I run
> blastpgp in a shell, it looks at the .ncbirc file in my home directory.
> 
> The third error I get is later in the run of stanaloneblast.pl:
> 

I'm not sure why you are getting that particular error, but it appears the
standaloneblast example script is not working and needs to be fixed.  I'll
consider that bug part of this report and we'll see if it can looked at.

> 
> Beginning mask-varying example...
> Performing BLAST with mask threshold = 50 %
> Bio/AlignIO/psi.pm: psi cannot be found
> Exception Can't locate Bio/AlignIO/psi.pm in @INC (@INC contains:
> /usr/lib/perl5/5.6.0/i386-linux /usr/lib/perl5/5.6.0
> /usr/lib/perl5/site_perl/5.6.0/i386-linux /usr/lib/perl5/site_perl/5.6.0
> /usr/lib/perl5/site_perl .) at
> /usr/lib/perl5/site_perl/5.6.0/Bio/AlignIO.pm line 379, <GEN6> line 89.
>  
> For more information about the AlignIO system please see the AlignIO
> docs.
> This includes ways of checking for formats at compile time, not run time
> Can't call method "write_aln" on an undefined value at
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Run/StandAloneBlast.pm line
> 698, <GEN6> line 89.
> 
> I do not know where the psi.pm file is/should be, but I did not get any
> other errors during install.
> 
> 
> Thank you for your assistance.
> 
> Saurabh.
> 
> 
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> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/