[Bioperl-l] Using BLAT in BioPerl

[Jason Stajich]

if it is indeed tempfile creation problems you can set the environment  
variable $TEMPDIR to specify where tempfiles are created on mac it  
should be /tmp or /var/tmp I would guess.

-jason
On Dec 16, 2008, at 10:20 AM, Dave Messina wrote:

> Hmm, tough to say what the problem is.
> One thing I noticed that seems a little odd is your blatSearch.pl  
> script
> appears to be running in your /Users/ directory, which is normally  
> owned by
> root and not writable by regular users.
>
> Also, it looks like it's attempting to create the temporary files in
> /var/folders, which as far as I remember is also owned by root.
>
> Not sure why running as root would necessarily cause a problem, but  
> it's an
> unusual scenario, so you might try running as a regular user in a  
> directory
> where you know you have write permissions.
>
> Otherwise, you could create a minimal example of your problem, such  
> as a
> single small query sequence, a single small database, and a test  
> script. You
> could post these in a bug report to Bugzilla so that someone can try  
> to
> reproduce your problem.
>
>
> Dave
>
>
>
>
> On Mon, Dec 15, 2008 at 17:56, oso <oso.oro at gmail.com> wrote:
>
>>
>> Error Message:
>> MSG: Blat call (blat
>> /var/folders/zK/zKXnWXt8G8epLqENEIdNkE+++TI/-Tmp-/wcjQruYe8A
>> /var/folders/zK/zKXnWXt8G8epLqENEIdNkE+++TI/-Tmp-/nePTpfPSKu - 
>> out=psl )
>> crashed: 65280
>>
>> STACK Bio::Tools::Run::Alignment::Blat::_run
>> /Library/Perl/5.8.8/Bio/Tools/Run/Alignment/Blat.pm:250
>> STACK Bio::Tools::Run::Alignment::Blat::run
>> /Library/Perl/5.8.8/Bio/Tools/Run/Alignment/Blat.pm:167
>> STACK main::get_orfs /Users/blatSearch.pl:50
>> STACK toplevel /Users/blatSearch.pl:29
>>
>> *******
>> I am running BioPerl version 1.5.2.
>>
>> Thanks for our help!
>>
>>
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Jason Stajich
jason at bioperl.org