[Bioperl-l] Blast return codes

[Keith James]

>>>>> "Matthew" == Matthew Laird <lairdm at sfu.ca> writes:

    Matthew> I did some more investigating and it's beginning to look
    Matthew> a lot more bizarre.  I changed the bioperl code to see if
    Matthew> the blast command was actually run regardless of the -1
    Matthew> return code.  And yes, blast did run and the result file
    Matthew> is there - it's only that perl is returning a -1 to
    Matthew> bioperl for some reason.

    Matthew> I was actually just speaking with someone in another lab
    Matthew> and he said he used to experience this problem too, his
    Matthew> solution was to just write his own modules. :)

    Matthew> So this certainly seems like some deep down perl/OS
    Matthew> voodoo.

Unfortunately, yes :( Especially as building Perl from source rather
than using RPMs seems to fix it.

    Matthew> I'd still be interested in hearing what envirnoment
    Matthew> variables to set to run t/StandAloneBlast.t.

I think it should pick up the standard blast environment variables
BLASTDIR and BLASTDATADIR via %ENV.

Keith

-- 

- Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -